Publications


2011-present

2017

Catherine A. Moreau, Saligram P. Bhargav, Hirdesh Kumar, Katharina A. Quadt, Henni Piirainen, Léanne Strauss, Jessica Kehrer, Martin Streichfuss, Joachim P. Spatz, Rebecca C. Wade, Inari Kursula and Friedrich Frischknecht

A unique profilin-actin interface is important for malaria parasite motility.
PLoS Pathog (2017), 13(5): e1006412 (Fulltext).

Nadinath B. Nillegoda, Antonia Stank, Duccio Malinverni, Neils Alberts, Anna Szlachcic, Alessandro Barducci, Paolo De Los Rios, Rebecca C. Wade and Bernd Bukau
Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.
eLife 2017;6:e24560 (Fulltext).

Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter and Rebecca C. Wade
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.
Nucleic Acids Res 2017 gkx277, (Fulltext).

Flavio Di Pisa, Giacomo Landi, Lucia Dello Iacono, Cecilia Pozzi, Chiara Borsari, Stefania Ferrari, Matteo Santucci, Nuno Santarem, Anabela Cordeiro-da-Silva, Carolina B. Moraes, Laura M. Alcantara, Vanessa Fontana, Lucio H. Freitas-Junior, Sheraz Gul, Maria Kuzikov, Birte Behrens, Ina Pöhner, Rebecca C. Wade, Maria Paola Costi and Stefano Mangani
Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.
Molecules (2017), 22(3):426, (Fulltext).

2016

S. Kashif Sadiq
Reaction-diffusion basis of retroviral infectivity.
Philos. Transactions Royal Soc. Lond. A: Math. Phys. Eng. Sci. (2016), 374:2080, (Abstract).

Mario Gundić, Antonija Tomić, Rebecca C. Wade, Mihaela Matovina, Zrinka Karačić, Saša Kazazić and Sanja Tomić
Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study.
Croat. Chem. Acta (2016), 89(2), DOI: 10.5562/cca2916, (Fulltext).

Rudi Tong, Rebecca C. Wade and Neil J. Bruce
Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties.
Proteins: Structure, Function, and Bioinformatics (2016), 84:1844-1858, (Abstract).

Daniela Schibich, Felix Gloge, Ina Pöhner, Patrik Björkholm, Rebecca C. Wade, Gunnar von Heijne, Bernd Bukau and Günter Kramer
Global profiling of SRP interaction with nascent polypeptides.
Nature (2016), 536:219-223, (Abstract).

Musa Ozboyaci, Michael Martinez, and Rebecca C. Wade
An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.
J. Chem. Theory Comput. (2016), 59:7598-7616, (Abstract).

Borsari et al.
Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs.
J. Med. Chem. (2016), 59:7598-7616, (Abstract).

Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade
Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.
J. Chem. Theory Comput. (2016), 12:4100–4113, (Fulltext).

Mehmet Ali Öztürk, Georgi V. Pachov, Rebecca C. Wade and Vlad Cojocaru
Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.
Nucl. Acids Res. (2016), 44:6599-6613, (Fulltext).

Klemens Wild, Gert Bange, Domantas Motiejunas, Judith Kribelbauer, Astrid Hendricks, Bernd Segnitz, Rebecca C. Wade, Irmgard Sinning
Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.
J. Mol Biol. (2016), 428:2880-2897, (Abstract).

Antonia Stank, Stefan Richter and Rebecca C. Wade
ProSAT+: visualizing sequence annotations on 3D structure.
PEDS (2016), 29:281-284, (Fulltext).

Sundar Raman Subramanian, Ettayapuram Ramaprasad Azhagiya Singam, Michael Berinski, Venkatesan Subramanian and Rebecca C. Wade
Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen.
J. Phys. Chem. (2016), 120:8580-8589, (Abstract).

Lensink et al.
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Proteins (2016), DOI:10.1002/prot.25007, (Abstract).

Antonia Stank, Daria B. Kokh, Jonathan C. Fuller and Rebecca C. Wade
Protein Binding Pocket Dynamics.
Acc. Chem. Res. (2016), 49:809-815, (Fulltext).

Musa Ozboyaci, Daria B. Kokh and Rebecca C. Wade
Three steps to gold: Mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.
Phys Chem Chem Phys. (2016) 18:10191-200, (Fulltext).

Georg Gdynia, Sven W. Sauer, Jürgen Kopitz, Dominik Fuchs, Katarina Duglova, Thorsten Ruppert, Matthias Miller, Jens Pahl, Adelheid Cerwenka, Markus Enders, Heimo Mairbäurl, Marcin M. Kamiński, Roland Penzel, Christine Zhang, Jonathan C. Fuller, Rebecca C. Wade, Axel Benner, Jenny Chang-Claude, Hermann Brenner, Michael Hoffmeister, Hanswalter Zentgraf, Peter Schirmacher and Wilfried Roth
The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration.
Nat. Commun. (2016) 7:10764, (Abstract).

Xiaofeng Yu, Daria B. Kokh, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade.
Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer.
In “High Performance Computing in Science and Engineering ’15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015”, Eds. Nagel, E. Wolfgang; Kröner, H. Dietmar; Resch, M. Michael. Springer International Publishing, Cham, Switzerland, (2016) pp. 255-264, (Abstract).

Rafiullah Rafiullah, Muhammad Aslamkhan, Nagarajan Paramasivam, Christian Thiel, Ghulam Mustafa, Stefan Wiemann, Matthias Schlesner, Rebecca C. Wade, Gudrun A. Rappold and Simone Berkel.
Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family.
J. Med. Genetics. (2016) 53:138-144, (Abstract).

Musa Ozboyaci, Daria B. Kokh, Stefano Corni and Rebecca C. Wade.
Modeling and simulation of protein–surface interactions: achievements and challenges.
Quart Rev Biophys (2016) 49, e4, (Fulltext).

Khalid Mohammed Khan, Mohammad A. Mesaik, Omer M. Abdalla, Fazal Rahim, Samreen Soomro, Sobia A. Halim, Ghulam Mustafa, Nida Ambreen, Ahmad Shukralla Khalid, Muhammad Taha, Shahnaz Perveen, Muhammad Tanveer Alam, Abdul Hameed, Zaheer Ul-Haq, Hayat Ullah, Zia Ur Rehman, Rafat Ali Siddiqui and Wolfgang Voelter.
The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies.
Bioorg. Chem. (2016) 64:21-28, (Abstract).

Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva and Rebecca C. Wade.
Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.
Biochim. Biophys. Acta (BBA) – General Subjects , (2016) 1860:67-78, (Abstract).

2015

Marta Rosa, Daria B. Kokh, Stefano Corni, Rebecca Wade and Rosa Di Felice.
Docking of DNA Duplexes on a Gold Surface.
J. Self-Assembly and Molecular Electronics (SAME), (2015) 3(7): 1-18, DOI: 10.13052/jsame2245-4551.2015009, (Fulltext).

Ghulam Mustafa, Prajwal P. Nandekar, Xiaofeng Yu and Rebecca C. Wade.
On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer
J. Chem. Phys., (2015) 143:243139, (Abstract).

Divita Garg, Stephane Skouloubris, Julien Briffotaux, Hannu Myllykallio and Rebecca C. Wade.
Conservation and Role of Electrostatics in Thymidylate Synthase.
Sci. Rep., (2015) 5:17356, (Abstract).

Julia Romanowska, Daria B. Kokh, and Rebecca C. Wade.
When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces.
Nano Lett., (2015) 15:7508-7513, (Abstract).

Antonija Tomić, Mykhaylo Berynskyy, Rebecca C. Wade and Sanja Tomić.
Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.
Mol. BioSyst., (2015) 11:3068-3080, (Abstract).

Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer and Bernd Bukau
Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation.
Nature, (2015) 524:247–251, (Fulltext).

Lei Liu, Rebecca C. Wade and Dieter W. Heermann
A multiscale approach to simulating the conformational properties of unbound multi-C2H2 zinc finger proteins.
Proteins, (2015) 83:1604-1615, (Fulltext).

Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter and Rebecca C. Wade
SDA 7: A modular and parallel implementation of the simulation of diffusional association software.
J. Comput. Chem., (2015) 36:1631-1645, (Fulltext).

Trinh V. Dinh, Willy V. Bienvenut, Eric Linster, Anna Feldman-Salit, Vincent A. Jung, Thierry Meinnel, Rudiger Hell, Carmela Giglione and Markus Wirtz
Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling.
Proteomics, (2015), 15:2426–2435, (Fulltext).

Christian Seybold, Menattallah Elserafy, Diana Rüthnick, Musa Ozboyaci, Annett Neuner, Benjamin Flottmann, Mike Heilemann, Rebecca C. Wade, and Elmar Schiebel
Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope.
J. Cell Biol., (2015) 209:843-861, (Fulltext).

Xiaofeng Yu, Michael Martinez, Annika L. Gable, Jonathan C. Fuller, Neil J. Bruce, Stefan Richter and Rebecca C. Wade.
webSDA: a web server to simulate macromolecular diffusional association.
Nucl. Acids Res., (2015) 43:W220-W224, (Fulltext).

Outi M. H. Salo-Ahen, Anna Tochowicz, Cecilia Pozzi, Daniela Cardinale, Stefania Ferrari, Yap Boum, Stefano Mangani, Robert M. Stroud, Puneet Saxena, Hannu Myllykallio, Maria Paola Costi, Glauco Ponterini and Rebecca C. Wade.
Hotspots in an Obligate Homodimeric Anticancer Target. Structural and Functional Effects of Interfacial Mutations in Human Thymidylate Synthase.
J. Med. Chem., (2015) 58:3572-3581, (Fulltext).

N.J. Bruce, Daria B. Kokh, M. Ozboyaci and Rebecca C. Wade.
Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.
In “Computational Trends in Solvation and Transport in Liquids-Lecture Notes, IAS Series, Schriften des Forschungszentrums Jülich”, Eds. Sutmann G, Grotendorst J, Gommpper G, Marx D. Forschungszentrum Jülich GmbH, Jülich, Germany (2015), vol. 28, pp. 259-280. (Fulltext).

Julia Romanowska, Daria B. Kokh, Jonathan C. Fuller and Rebecca C. Wade.
Computational Approaches for Studying Drug Binding Kinetics.
In “Kinetics and Thermodynamics of Drug Binding Kinetics and Thermodynamics of Drug Binding”, Eds. Keserü GM, Swinney DC. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, (2015) vol. 65, pp. 7508-7513. (Fulltext).

Xiaofeng Yu, Vlad Cojocaru, Ghulam Mustafa, Outi M. H. Salo-Ahen, Galina I. Lepesheva and Rebecca C. Wade.
Dynamics of CYP51: implications for function and inhibitor design.
J. Molec. Recogn., (2015) 28:59-73. (Fulltext).

Jonathan C. Fuller, Michael Martinez, Stefan Henrich, Antonia Stank, Stefan Richter and Rebecca C. Wade.
LigDig: a web server for querying ligand-protein interactions.
Bioinformatics, (2015) 31:1147-1149. (Fulltext).

2014

Paolo Mereghetti, Michael Martinez and Rebecca C. Wade.
Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.
BMC Biophysics, (2014) 7(1):4. (Fulltext).

Jonathan C. Fuller, Michael Martinez and Rebecca C. Wade.
On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics.
PLOS ONE, (2014) 9(8):e104778. (Fulltext).

Ghulam Mustafa, Xiaofeng Yu and Rebecca C. Wade.
Structure and Dynamics of Human Drug-Metabolizing Cytochrome P450 Enzymes.
In Drug Metabolism Prediction, (2014) pages 75-102. Wiley-VCH Verlag GmbH & Co. KGaA. (Fulltext).

2013

Linda Gombos, Annett Neuner, Mykhaylo Berynskyy, Luca L. Fava, Rebecca C. Wade, Carsten Sachse and Elmar Schiebel.
GTP regulates the microtubule nucleation activity of γ-tubulin.
Nat Cell Biol., (2013) 15:1317-27. (Abstract).

Arzu Sandikci, Felix Gloge, Michael Martinez, Matthias P. Mayer, Rebecca Wade, Bernd Bukau and Guenter Kramer.
Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.
Nat Struct Mol Biol., (2013) 20:843-50. (Abstract).

Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer and Rebecca C Wade.
Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria.
PLoS Comput Biol., (2013) 9:e1003159. (Fulltext).

Anna Feldman-Salit, Silvio Hering, Hanan L Messhia, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans V. Westerhoff, Bernd Kriekemeyer, Rebecca C Wade and Tomas Fiedler.
Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria.
J. Biol. Chem., (2013) 288:21295-306. (Abstract).

Daria B Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann and Rebecca C Wade.
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins.
J. Chem Inf Model, (2013) 53:1235-52. (Abstract).

Jessica Balbo, Paolo Mereghetti, Dirk-Peter Herten and Rebecca C Wade.
The Shape of Protein Crowders is a Major Determinant of Protein Diffusion.
Biophys. J., (2013) 104:1576-84. (Abstract).

Paolo Mereghetti and Rebecca C. Wade.
Brownian dynamics simulation of protein diffusion in crowded environments.
AIP Conf. Proc., (2013) 1518:511-516. (Abstract).

Xiaofeng Yu, Vlad Cojocaru and Rebecca C. Wade.
Conformational diversity and ligand tunnels of mammalian cytochrome P450s.
Biotechnology and Applied Biochemistry, (2013) 60:134-45. (Fulltext).

Divita Garg, Alexander V. Beribisky, Glauco Ponterini, Alessio Ligabue, Gaetano Marverti, Andrea Martello, M. Paola Costi, Michael Sattler and Rebecca C. Wade.
Translational repression of thymidylate synthase by targeting its mRNA.
Nucleic Acids Res., (2013) 41 (7): 4159-4170. (Fulltext).

Mykhaylo Berynskyy and Rebecca C. Wade.
Treating conformational flexibility in protein-protein docking.
Curr. Phys. Chem., (2013) 3:27-35. (Fulltext).

Stefania Ferrari, Marco Ingrami, Fabrizia Soragni, Rebecca C. Wade and M. Paola Costi.
Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors.
Bioorg Med Chem Lett., (2013) 23:663-8. (Abstract).

2012

Yuki Oguchi, Eva Kummer, Fabian Seyffer, Mykhaylo Berynskyy, Benjamin Anstett, Regina Zahn, Rebecca C Wade, Axel Mogk and Bernd Bukau.
A tightly regulated molecular toggle controls AAA+ disaggregase.
Nat Struct Mol Biol., (2012) 19:1338-46. (Abstract).

Giorgia Brancolini, Daria B. Kokh, Luigi Calzolai, Rebecca C. Wade and Stefano Corni.
Docking of Ubiquitin to Gold Nanoparticles.
ACS Nano, (2012) 6:9863-78. (Abstract).

Paolo Mereghetti and Rebecca C. Wade.
Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions.
J. Phys. Chem. B, (2012) 116:8523-8533. (Abstract).

Lada Biedermannová, Zbynek Prokop, Artur Gora, Eva Chovancova, Mihaly Kovacs, Jiri Damborsky and Rebecca C. Wade.
A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB.
J. Biol. Chem., (2012) 287:29062-74. (Abstract).

Matthias Stein, Manohar Pilli, Sabine Bernauer, Bianca H. Habermann, Marino Zerial and Rebecca C. Wade.
The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity.
PLoS ONE, (2012) 7:e34870. (Fulltext).

Anna Feldman-Salit, Markus Wirtz, Esther D. Lenherr, Christian Throm, Michael Hothorn, Klaus Scheffzek, Rüdiger Hell and Rebecca C. Wade.
Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex Regulate Cysteine Biosynthesis in Arabidopsis thaliana.
Structure, (2012) 20:292-302. (Abstract).

Vlad Cojocaru, Peter J. Winn and Rebecca C. Wade.
Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9.
Curr. Drug. Metab., (2012) 13:143-154. (Abstract).

2011

Daniela Cardinale, Giambattista Guaitoli, Donatella Tondi, Rosaria Luciani, Stefan Henrich, Outi M. H. Salo-Ahen, Stefania Ferrari, Gaetano Marverti, Davide Guerrieri, Alessio Ligabue, Chiara Frassineti, Cecilia Pozzi, Stefano Mangani, Dimitrios Fessas, Remo Guerrini, Glauco Ponterini, Rebecca C. Wade and Maria Paola Costi.
Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase.
Proc. Natl. Acad. Sci. USA, (2011) 108:13889-13890, E542-E549. (Fulltext).

Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom and Rebecca C. Wade.
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9.
PLoS Comput. Biol., (2011) 7(8):e1002152. (Fulltext) ; (Cover Figure).

Outi M.H. Salo-Ahen and Rebecca C. Wade.
The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations.
Proteins, (2011) 79:2886-99. (Abstract).

Paolo Mereghetti and Rebecca C. Wade.
Diffusion of hydrophobin proteins in solution and interactions with a graphite surface.
BMC Biophysics, (2011) 4:9. (Fulltext).

Sundar Raman S., R. Gopalakrishnan, Rebecca C. Wade and V. Subramanian.
Structural Basis for the Varying Propensities of Different Amino Acids To Adopt the Collagen Conformation.
J. Phys. Chem. B., (2011) 115:2593-2607. (Abstract).

Daria B. Kokh, Rebecca C. Wade and Wolfgang Wenzel.
Receptor flexibility in small-molecule docking calculations.
WIREs Comput. Molec. Sci., (2011) 1:298-314. (Fulltext).

Paolo Mereghetti, Daria B. Kokh, J. Andrew McCammon and Rebecca C. Wade.
Diffusion and association processes in biological systems: theory, computation and experiment.
BMC Biophysics, (2011) 4:2. (Fulltext).

Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
On the structure and dynamics of the complex of the nucleosome and the linker histone.
Nucl. Acid. Res., (2011) 39 (12): 5255-5263. (Fulltext).

Stefania Ferrari, Federica Morandi, Domantas Motiejunas, Erika Nerini, Stefan Henrich, Rosaria Luciani, Alberto Venturelli, Sandra Lazzari, Samuele Calo, Shreedhara Gupta, Veronique Hannaert, Paul A. M. Michels, Rebecca C. Wade and M. Paola Costi.
Virtual Screening Identification of Nonfolate Compounds, Including a CNS Drug, as Antiparasitic Agents Inhibiting Pteridine Reductase.
J. Med. Chem., (2011) 54:211-221. (Abstract).

Ori Cohavi, Dana Reichmann, Renne Abramovich, Alexander B. Tesler, Giuliano Bellapadrona, Daria B. Kokh, Rebecca C. Wade, Alexander Vaskevich, Israel Rubinstein and Gideon Schreiber.
A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces.
Chem. Eur. J., (2011) 17:1327-1336. (Abstract).

2002-2010

2010

Sandeep Kaur-Ghumaan, Lennart Schwartz, Reiner Lomoth, Matthias Stein and Sascha Ott.
Katalytische Wasserstofferzeugung an einem einkernigen Eisen(II)-Carbonylkomplex als kleinstes funktionelles Modell für das aktive Zentrum von [FeFe]-Hydrogenasen.
Angew. Chem., (2010) 122:8207-8211. (Abstract).

Sandeep Kaur-Ghumaan, Lennart Schwartz, Reiner Lomoth, Matthias Stein and Sascha Ott.
Catalytic Hydrogen Evolution from Mononuclear Iron(II) Carbonyl Complexes as Minimal Functional Models of the [FeFe] Hydrogenase Active Site.
Angew. Chem. Intl., (2010) 49:8033-8036. (Abstract).

Simone Loescher, Antje Gebler, Matthias Stein, Oliver Sanganas, Thorsten Buhrke, Ingo Zebger, Holger Dau, Baerbel Friedrich, Oliver Lenz and Michael Haumann.
Protein–Protein Complex Formation Affects the Ni–Fe and Fe–S Centers in the H2-Sensing Regulatory Hydrogenase from Ralstonia eutropha H16.
Chem. Phys. Chem., (2010) 11:1297-1306. (Abstract).

Markus Wirtz, Hannah Birke, Corinna Heeg, Christopher Mueller, Fabian Hosp, Christian Throm, Anna Feldman-Salit, Karsten Rippe, Gabriele Petersen, Rebecca C. Wade, Vladimir Rybin, Klaus Scheffzek and Ruediger Hell.
Structure and Function of the Hetero-oligomeric Cysteine Synthase Complex in Plants.
J. Biol. Chem., (2010) 285:32810-32817. (Abstract).

Paolo Mereghetti, Razif R. Gabdoulline and Rebecca C. Wade.
Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties.
Biophys. J., (2010) 99:3782-3791. (Abstract).

Divita Garg, Stefan Henrich, Outi M. H. Salo-Ahen, Hannu Myllykallio, Maria P. Costi and Rebecca C. Wade.
Novel Approaches for Targeting Thymidylate Synthase To Overcome the Resistance and Toxicity of Anticancer Drugs.
J. Med. Chem., (2010) 53:6539-6549. (Abstract).

Edda Klipp, Rebecca C. Wade and Ursula Kummer.
Biochemical network-based drug-target prediction.
Curr. Op. Biotech., (2010) 21:511-516. (Abstract).

Daria B. Kokh, Stefanio Corni, Peter J. Winn, Martin Hoefling, Key E. Gottschalk and Rebecca C. Wade.
ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent.
J. Chem. Theory Comput., (2010) 6:1753-1768. (Abstract).

Sean I. O’Donoghue, David S. Goodsell, A. S. Frangakis, F. Jossinet, Roman A. Laskowski, Michael Nilges, Helen R. Saibil, Andrea Schafferhans, Rebecca C. Wade, Eric Westhof and Art J. Olson.
Visualization of macromolecular structures.
Nature Methods, (2010) 7:42-55. (Abstract).

Olivier Michielin and Rebecca C. Wade.
Foreword preface to the jmr special issue on ‘dynamic aspects of molecular recognition’.
J. Mol. Recogn., (2010) 23:101. (Abstract).

Daniela Cardinale, Outi M.H. Salo-Ahen, Stefania Ferrari, Glauco Ponterini, G. Crucicali, E. Carotati, Anna Tochowicz, Stefano Mangani, Rebecca C. Wade and M. Paola Costi.
Homodimeric enzymes as drug targets.
Curr. Med. Chem., (2010) 17:826-846. (Abstract).

Daniela Cardinale, Outi M.H. Salo-Ahen, G. Guatoli, Stefania Ferrari, Alberto Venturelli, Silvia Franchini, R. Battini, Rebecca C. Wade and M. Paola Costi.
Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding.
Prot. Eng. Des. Sel., (2010) 23:81-89. (Abstract).

Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields.
Mol. BioSyst., (2010) 6:162-174. (Abstract).

Ori Cohavi, Stefano Corni, Francesca De Rienzo, Rosa Di Felice, Kay E. Gottschalk, Martin Hoefling, Daria Kokh, Elisa Molinari, Gideon Schreiber, Alexei Vaskevich and Rebecca C. Wade.
Protein-surface interactions: challenging experiments and computations.
J. Mol. Recogn., (2010) 23:259-262. (Abstract).

Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
Kinetics of biomacromolecular complex formation: Theory and experiment.
In ” Protein-Protein Complexes: Analysis, Modeling and Drug Design”, Ed. M. Zacharias, World Scientific/Imperial College Press, (2010) pages 89-119. Contents.

Stefan Henrich, Outi M.H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani and Rebecca C. Wade.
Computational approaches to identifying and characterizing protein binding sites for ligand design.
J. Mol. Recogn., (2010) 23:209-219. (Abstract).

Stefan Henrich, Isabella Feierberg, Ting Wang, Niklas Blomberg and Rebecca C. Wade.
Comparative binding energy analysis for binding affinity and target selectivity prediction.
Proteins, (2010) 78:135-153. (Abstract).

2009

B. Huang.
metapocket: a meta approach to improve protein ligand binding sites prediction.
Omics, (2009) 13(4):325-330. (Abstract).

Christian Müller, Maria Antonia Gomez-Zurita Frau, Dario Ballinari, Sonia Colombo, Alessandro Bitto, Enzo Martegano, Cristina Arnold, Anske Stephanie van Neuren, Matthias Stein, Jörg Weiser, Carlo Battistini and Francesco Peri.
Design, synthesis, and biological evaluation of levoglucosenome-derived ras activation inhibitors.
ChemMedChem, (2009) 4:524-528. (Abstract).

Pradyuma S. Singh, Hans C. Rudbeck, Ping Huang, Salah Ezzaher, Lars Eriksson, Matthias Stein, Sascha Ott and Reiner Lomoth.
(i,0) mixed-valence state of a diiron complex with pertinence to the [fefe]-hydrogenase active site: An ir, epr, and computational study.
Inorganic Chemistry, (2009) 48:10883-10885. (Abstract).

Martina Pavlova, Martin Klvana, Zbynek Prokop, Radka Chaloupkova, Pavel Banas, Michal Otyepka, Rebecca C. Wade, Masataka Tsuda, Yuji Nagata and Jiri Damborsky.
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
Nature Chem. Biol., (2009) 5:727-733. (Abstract).

Martin Klvana, Martina Pavlova, Tana Koudelakova, Radka Chaloupkova, Pavel Dvorak, Alena Stsiapanava, Michal Kuty, Ivana Kuta-Smatanova, Jan Dohnalek, Petr Kulhanek, Rebecca C. Wade and Jiri Damborsky.
Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.
J. Mol. Biol., (2009) 392:1339-1356. (Abstract).

Razif R. Gabdoulline and Rebecca C. Wade.
On the contributions of diffusion and thermal activation to electron transfer between phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.
J. Am. Chem. Soc., (2009) 131:9230-9238. (Abstract).

Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
Computational simulations of protein-protein and protein-nucleic acid association.
In ” Computational Protein-Protein Interactions”, Eds. R. Nussinov and G. Schreiber, Taylor and Francis Group LLC, Boca Raton, (2009) pages 109-128.

Georgi V. Pachov and Rebecca C. Wade.
Docking of a linker histone to the nucleosome with flexible linker dnas.
Biophys. J., (2009) 96:83a-84a. (Abstract).

Daria B. Kokh, Bingding Huang, Rebecca C. Wade and Peter J. Winn.
Modeling of protein adsorption on a metal surface: Brownian dynamics simulations.
Biophys. J., (2009) 96:298a-299a. (Abstract).

Anna Feldman-Salit, Markus Wirtz, Ruediger Hell and Rebecca C. Wade.
A mechanistic model of the cysteine synthase complex.
JMB, (2009) 386(1):37-59. (Abstract).

Anna Feldman-Salit and Rebecca C. Wade.
Molecular recognition, computation and modeling of.
In Encyclopedia of Chemical Biology. Wiley. (Link).

2008

Woelkart K., Salo-Ahen O. M. and Bauer R.
CB receptor ligands from plants.
Curr Top Med Chem., (2008) 8(3):173-86. (Abstract).

Salo-Ahen O. M.
Editorial.
Curr Top Med Chem., (2008) 8(3):172.

J. Hegermann, S. Halbedel, R. Dumke, J. Regula, R.R. Gabdoulline, F. Mayer, J. Stuelke and R. Herrmann.
The acidic, glutamine-rich mpn474 protein of mycoplasma pneumoniae is surface exposed and covers the complete cell.
Microbiology, (2008) 154:1185-1192. (Fulltext).

Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
webpipsa: a web server for the comparison of protein interaction properties.
Nucleic Acids Res., (2008) 36:W276-80. (Fulltext).

A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade and U. Kummer.
SYCAMORE-a systems biology computational analysis and modeling research environment.
Bioinformatics, (2008) 24:1463-1464. (Fulltext).

Heidrun Witan, Andreas Kern, Ingrid Koziollek-Drechsler, Rebecca Wade, Christian Behl and Albrecht M. Clement.
Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-Superoxide dismutase induces toxicity independent of protein aggregation.
Human Molecular Genetics, (2008) 17:1373-1385. (Abstract).

Domantas Motiejunas, Razif R. Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn and Rebecca C. Wade.
Protein-protein docking by simulating the process of association subject to biochemical constraints.
Proteins, (2008) 71:1955-1969. (Abstract).

Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Calculating enzyme kinetic parameters from protein structures.
Biochem. Soc. Trans., (2008) 36:51-54. (Abstract).

Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade and Sanja Tomic.
Mechanism of auxin interaction with auxin binding protein (ABP1): a molecular dynamics simulation study.
Biophys. J., (2008) 94:27-37. (Abstract)

Stefan Henrich, Stefan Richter and Rebecca C. Wade.
On the use of PIPSA to guide target-selective drug design.
ChemMedChem, (2008) 3:413-417. (Link).

2007

Eilers G., Schwartz L., Stein M., Zampella G., de Gioia L., Ott S. and Lomoth R.
Ligand versus metal protonation of an iron hydrogenase active site mimic.
Chemistry., (2007) 13 (25):7075-84. (Fulltext).

Simone Loescher, Lennart Schwartz, Matthias Stein, Sascha Ott and Michael Haumann.
Facilitated hydride binding in an fe-fe hydrogenase active?site biomimic revealed by x-ray absorption spectroscopy and dft calculations.
Inorg. Chem., (2007) 46 (26):11094-11105. (Fulltext).

Razif R. Gabdoulline, Matthias Stein and Rebecca C. Wade.
qPIPSA: Relating enzymatic kinetic parameters and interaction fields.
BMC Bioinformatics, (2007) 8:373. (Fulltext).

Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Bridging from molecular simulation to biochemical networks.
Curr. Op. Struct. Biol., (2007) 17:166-172. (Abstract).

Rebecca C. Wade.
Exploring biomolecular recognition by modelling and simulation.
In Modeling and Simulation in Science. Proceedings of the 6th International Workshop on Data Analysis in Astronomy “Livio Scarsi”, (2007) pages 150-153. Eds. V. Di Gesu, G. Lo Bosco and M.C. Maccarone., World Scientific Publishing Co..

Georgi Pachov, Razif R. Gabdoulline and Rebecca C. Wade.
Simulation of linker histone-chromatin interactions.In ‘From Computational Biophysics to Systems Biology (CBSB2007)’, John von Neumann Institute for Computing, Juelich, NIC Series 36:69-74. (Fulltext).

Ting Wang and Rebecca C. Wade.
On the use of elevated temperature in simulations to study protein unfolding mechanisms.
J. Chem. Theory Comput., (2007) 3:1476-1483. (Abstract).

Peter J. Winn, Mai Zahran, James N.D. Battey, Yanxiang Zhou, Rebecca C. Wade and Amit Banerjee.
Structural and electrostatic properties of ubiquitination and related pathways.
Frontiers in Bioscience, (2007) 12:3419-3430. (Abstract).

Sanja Tomic, Branimir Bertosa, Ting Wang and Rebecca C. Wade.
COMBINE analysis of the specificity of binding of ras proteins to their effectors.
Proteins, (2007) 67:435-447. (Abstract).

Peter J .Winn, Mai Zahran and Rebecca C. Wade.
Comparisons of the protein electrostatic potentials as a means to understanding function.
In Workshop on Protein Folding and Drug Design, (2007) volume 165 of Proceedings of the International School of Physics “Enrico Fermi”, (2007) pages 207-219. Eds. Broglia, R.A., Serrano, L., Tiana, G., Societa Italiana di Fisica, Bologna, Italy. ISBN 978-1-58603-792-5.

Andrey Karyakin, Domantas Motiejunas, Rebecca C. Wade and Christiane Jung.
FTIR studies of the redox partner interaction in cytochrome P450. the Pdx-P450cam couple.
Biochimica et Biophysica Acta. General Subjects, (2007) 1770:420-431 . (Abstract).

Matthias Stein, Razif R. Gabdoulline, Bruno Besson and Rebecca C. Wade.
The estimation of kinetic parameters in systems biology by comparing molecular interaction fields of enzymes.
In Beilstein Proceedings of the 2nd Conference on Experimental Standard Conditions of Enzyme Characterizations,Ruedesheim, 19-23 March, 2006, (2007) pages 237-253. (Fulltext).

Vlad Cojocaru, Peter J. Winn and Rebecca C. Wade.
The ins and outs of cytochrome P450s.
Biochimica et Biophysica Acta. General Subjects, (2007) 1770:390-401 . (Abstract).

Domantas Motiejunas and Rebecca C. Wade.
Structural, energetic, and dynamic aspects of ligand-receptor interactions.
In Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 193-213. Eds. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford.
ISBN 0080445136.

Gabriele Cruciani, Emanuele Carosati, Rebecca C. Wade and Massimo Baroni.
Characterization of protein-binding sites and ligands using molecular interaction fields.
In Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 237-253. Eds. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford.
ISBN 0080445136.

2006

Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade.
Integrating structural and kinetic enzymatic information in systems biology.In NIC Workshop 2006 ‘From Computational Biophysics to Systems Biology’,6-9 June, John von Neumann Institute for Computing, Juelich, volume 34 of NIC Series, (2006) pages 129-132. (Abstract & Full Text).

Schleinkofer K., Wang T. and Wade R.C.
Molecular docking.
In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, (2006) pages pp1149-1153. Ed. Ganten,D. and Ruckpaul, K. Springer.

Razif R. Gabdoulline, Stefan Ulbrich, Stefan Richter and Rebecca C. Wade.
ProSAT2-protein structure annotation server.
Nucl. Acids. Res., (2006) 34:W79-W83. (Abstract & Full Text).

Henrik R. Hallingbaeck, Razif R. Gabdoulline and Rebecca C. Wade.
Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking.
Biochemistry, (2006) 45:2940-2950. (Abstract).

Alexander Spaar, Christian Dammer, Razif R. Gabdoulline, Rebecca C. Wade and Volkhard Helms.
Diffusional encounter of barnase and barstar.
Biophys. J., (2006) 90:1913-1924. (Abstract).

Ting Wang and Rebecca C. Wade.
Force field effects on a beta-sheet protein domain structure in thermal unfolding simulations.
J. Chem. Theory Comput., (2006) 2:140-148. (Abstract).

Karl J. Jalkanen, Vibeke Würtz-Jürgensen, Anetta Claussen, Abdoul Rahim, G. M. Jensen, Rebecca C. Wade, Frederico Nardi, Christiane Jung, Ivan M. Degtyarenko, Risto M. Nieminen, Frank Herrmann, Michaela Knapp-Mohammady, Thomas A. Niehaus, Kenneth Frimand and Sandor Suhai.
Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach.
Intl. J. Quant. Chem., (2006) 106:1160-1198. (Abstract).

2005

Rebecca C. Wade, Domantas Motiejunas, Karin Schleinkofer, Peter J. Winn Sudarko, Amit Banerjee, Andrei Kariakin and Christiane Jung.
Multiple molecular recognition mechanisms. cytochrome P450-a case study.
Biochimica et Biophysica Acta, (2005) 1754:239-244. (Abstract).

Rebecca C. Wade.
Calculation and application of molecular interaction fields.
In Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction, (2005) pages Ch. 2, pp27-42. Ed. Cruciani, G., Wiley-VCH Weinheim, ISBN 3-527-31087-8. (Publisher Link).

J. Andrew McCammon and Rebecca C. Wade.
Pushing the limits: Editorial overview.
Curr. Opin. Struct. Biol., (2005) 15:135-136. (Link).

Karin Schleinkofer, Peter J. Winn Sudarko, Susanna K. Lüdemann and Rebecca C. Wade.
Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?
EMBO Reports, (2005) 6:584-589. (Abstract).

Rebecca C. Wade.
Recognition highlights and commentaries.
J. Mol. Recognit., (2005) 18:191. (Link).

Jan Kmunicek, Kamila Hynkova, Tomas Jedlicka, Yuji Nagata, Ana Negri, Federico Gago, Rebecca C. Wade and Jiri Damborsky.
Quantitative analysis of substrate specificity of haloalkane dehalogenase linB from sphingomonas paucimobilis UT26.
Biochemistry, (2005) 44:3390-3401. (Abstract).

Peter J. Winn, James N. Battey, Karin Schleinkofer, Amit Banerjee and Rebecca C. Wade.
Issues in high-throughput comparative modelling: A case study using the ubiquitin E2 conjugating enzymes.
Proteins, (2005) 58:367-375. (Link).

Lutz P. Ehrlich, Michael Nilges and Rebecca C. Wade.
The impact of protein flexibility on protein-protein docking.
Proteins, (2005) 58:126-133. (Abstract).

2004

Rebecca C. Wade, Stefan Henrich and Ting Wang.
Using 3D protein structures to derive 3D-QSARs.
Drug Discovery Today: Technologies, (2004) 1(3):241-246. (Abstract).

Karin Schleinkofer, Urs Wiedemann, Livia Otte, Ting Wang, Gerd Krause, Hartmut Oschkinat and Rebecca C. Wade.
Comparative structural and energetic analysis of ww domain-peptide interactions.
J. Mol. Biol., (2004) 344:865-881. (Abstract).

Peter J. Winn, Tomasz L. Religa, James D. Battey, Amit Banerjee and Rebecca C. Wade.
Determinants of functionality in the ubiquitin conjugating enzyme family.
Structure, (2004) 12:1563-74. (Abstract) ; (The Ubiquitin and Ubiquitin-like Protein Web Resource).

Ting Wang, Sanja Tomic, Razif R. Gabdoulline and Rebecca C. Wade.
How optimal are the binding energetics of barnase and barstar?
Biophys. J., (2004) 87:1618-1630. (Abstract).

Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade, Marco Sola and M Cristina Menziani.
Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins.
Cell Mol. Life Sci, (2004) 61:1123-1142. (Abstract).

Rebecca C. Wade, Peter J. Winn, Ilme Schlichting and Sudarko.
A survey of active site access channels in cytochromes P450.
J. Inorg. Biochem., (2004) 98:1175-1182. (Abstract).

Jiri Damborsky, Jan Kmunicek, Tomas Jedlicka, Santos Luengo, Federico Gago, Angel R. Ortiz and Rebecca C. Wade.
Rational re-design of haloalkane dehalogenases guided by comparative binding energy analysis.
I (2004)n Enzyme functionality: Design, Engineering and Screening pages pp79-96. Ed. A. Svendsen, Marcel Dekker, New York. ISBN: 0-8247-4709-7.

2003

Tomasz Zemojtel, Rebecca C. Wade and Thomas Dandekar.
In search of the prototype of nitric oxide synthase.
FEBS Letts., (2003) 554:1-5. (Abstract).

Stefania Ferrari, M. Paola Costi and Rebecca C. Wade.
Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase.
Chemistry & Biology, (2003) 10:1183-1193. (Abstract).

Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade, Michael Ramek, Stavroula Piperaki, Anna Tsantili-Kakoulidou and Sanja Tomic.
A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: Application to auxins.
Chem. Inf. Comput. Sci., (2003) 43:1532-1541. (Abstract).

Timm Essigke, G. Matthias Ullmann and Rebecca C. Wade.
What determines the redox potential of ferredoxins?
In “Proceedings of the 13th International Conference on Cytochromes P450″, (2003) pages 25-30. Monduzzi Editore, Bologna .

Jan Kmunicek, Michal Bohac, Santos Luengo, Federico Gago, Rebecca C. Wade and Jiri Damborsky.
Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.
J. Comput. Aided Mol. Des., (2003) 17:299-311. (Abstract).

Razif Gabdoulline, Rebecca C. Wade and Dirk Walther.
MolSurfer: a macromolecular interface navigator.
Nucleic Acids Res., (2003) 31:3349-3351. (Abstract) ; (Fulltext) ; (Webserver).

Razif Gabdoulline, Ursula Kummer, Lars F. Olsen and Rebecca C. Wade.
Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations.
Biophys. J., (2003) 85:1421-1428. (Fulltext) ; (Movie).

Razif Gabdoulline, Rene Hoffmann, Florian Leitner and Rebecca C. Wade.
ProSAT: Functional annotation of protein 3D structures.
Bioinformatics, (2003) 19:1723-1725. (Abstract) ; (Webserver).

Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez and Rebecca C.
DSMM – a database of simulated molecular motions.
Nucleic Acids Res., (2003) 31:456-457. (Abstract) ; (Fulltext) ; (Database).

Ting Wang and Rebecca C. Wade.
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.
Proteins, (2003) 50:158-169. (Abstract).

2002

Eric Deprez, Edward Gill, Volkhard Helms, Rebecca C. Wade and Gaston Hui Bon Hoa.
Specific and non-specific effects of potassium cations on substrate-protein interactions in cytocromes P450cam and P450lin.
J. Inorg. Biochem., (2002) 91:597-606. (Abstract).

Ting Wang and Rebecca C. Wade.
Comparative binding energy (COMBINE) analysis of OppA-peptide complexes.
Med. Chem., (2002) 45:4828-4837. (Abstract).

Peter J. Winn, Susanna K. Lüdemann, Ralph Gauges, Valere Lounnas and Rebecca C. Wade.
Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine.
Proc. Natl. Acad. Sci. USA, (2002) 99:5361-5366. (Abstract) ; (Full text).

Razif R. Gabdoulline and Rebecca C. Wade.
Biomolecular diffusional association.
Curr. Opin. Struct. Biol., (2002) 12:204-213. (Abstract).

Amit Banerjee and Rebecca C. Wade.
Elusive recognition determinants for ubiquitination.
J. Molec. Recogn., (2002) 15:3-5. (Abstract).

Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade and M. Cristina Menziani.
Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors.
In Handbook of Copper Pharmacology and Toxicology, (2002) pages pp. 53-80. Ed. E. J. Massaro, Humana Press, Totowa, New Jersey.

1988-2001

Wade Group Publications at EMBL : 1992-2001

Wade Publications : 1988-1991


2001

De Rienzo, F., Gabdoulline,R.R., Menziani,M.C., De Benedetti, P.G. and Wade,R.C.
Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F
Biophys. J. (2001) 81, 3090-3104.

Kmunicek, J., Luengo,S., Gago,F., Ortiz, A.R., Wade,R.C. and Damborsky,J.
Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter Autotrophicus GJ10
Biochemistry (2001) 40, 8905-8917, 11288.

Wang,T. and Wade,R.C.
Comparative Binding Energy (COMBINE) analysis of Influenza Neuraminidase-Inhibitor Complexes
J. Med. Chem. (2001) 44, 961-971.

Gabdoulline,R.R. and Wade,R.C.
Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations
J. Mol. Biol. (2001) 306, 1139-1155.

Luedemann,S.K., Gabdoulline, R.R., Lounnas,V. and Wade,R.C.
Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms
Internet. J. Chem. (2001) 4, 6. [ISSN: 1099-8292] http://www.ijc.com/articles/2001v4/6/

Wade,R.C., Gabdoulline, R.R. and De Rienzo, F.
Protein Interaction Property Similarity Analysis
Intl. J. Quant. Chem. (2001) 83, 122-127.

Tomic,S. and Wade,R.C.
COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Data Sets
Croat. Chem. Acta. (2001) 74, 295-314.

Ehrlich,L.P. and Wade,R.C.
Protein-Protein Docking
Rev. Comp. Chem. (2001) 17, 61-97.

Jalkanen,K.J., Nieminen,R.M., Frimand,K., Bohr,J., Bohr, H., Wade,R.C., Tajkhorshid, E. and Suhai,S.
A Comparison of Aqueous Solvent Models Used in the Calculation of the Raman and ROA spectra of L-alanine
Chem. Phys. (2001) 265, 125-151.

Wang,T. and Wade,R.C.
COMBINE 3D-QSAR analysis of Influenza Neuraminidase Inhibitors
In “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships” Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp78-82.

Wade,R.C.
Derivation of QSARs using 3D Structural Models of Protein-ligand complexes by COMBINE Analysis
In “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships” Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp23-28.

2000

Luedemann,S.K., Lounnas, V. and Wade, R.C.
How do substrates enter and products exit the buried active site of cytochrome P450cam ?
1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms

J. Mol. Biol. (2000) 303, 797-811.

Luedemann,S.K., Lounnas, V. and Wade, R.C.
How do substrates enter and products exit the buried active site of cytochrome P450cam ?
2. Steered molecular dynamics and adiabatic mapping of substrate pathways

J. Mol. Biol. (2000) 303, 813-830.

Das, B., Helms,V., Lounnas, V. and Wade, R.C.
Multicopy molecular dynamics simulations suggest how to reconcile crystallographic
and product formation data for camphor enantiomers bound to cytochrome P-450cam

J. Inorg. Biochem. (2000) 81,121-31

De Rienzo, F., Gabdoulline,R.R., Menziani,M.C. and Wade,R.C.
Blue Copper Proteins: A Comparative Analysis of their Molecular Interaction Properties
Protein Science (2000) 9, 1439-54.

Nardi,F., Kemmink,J., Sattler,M. and Wade,R.C.
The cisProline(i-1)-Aromatic(i) Interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches
J. Biomol. NMR (2000) 17, 63-77.

Lamotte-Brasseur,J., Dubus, A. and Wade,R.C.
pKa calculations for Class C beta-lactamases: The role of Tyr-150
Proteins (2000) 40, 23-28.

Tomic,S., Nilsson,L. and Wade,R.C.
Nuclear receptor-DNA binding specificity: a COMBINE and Free-Wilson QSAR analysis
J. Med. Chem. (2000) 43, 1780-1792.

Tomic,S., Nilsson,L. and Wade,R.C.
COMBINE and Free-Wilson QSAR analysis of nuclear receptor – DNA binding
In “Molecular Modeling and Prediction of Bioactivity”
Eds. Gundertofte K. and Jorgensen F. S.
Plenum (2000), Kluwer Academic/Plenum Publishers, New York, 269-270.

1999

Gabdoulline,R.R., Wade,R.C. and Walter,D.
MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes
Trends in Biochem. Sci. (1999) 24, 285-287.

Blomberg,N., Gabdoulline,R.R., Nilges,M. and Wade,R.C.
Classification of Protein Sequences by Homology Modeling and Quantitative Analysis of Electrostatic Similarity
Proteins (1999) 37, 379-387.

Nielsen,J.E., Andersen,K.V., Honig,B., Hooft,R.W.W., Klebe,G., Vriend,G. and Wade,R.C.
Improving macromolecular electrostatics calculations
Protein Eng (1999) 12, 657-662.

Linge,J.P., Nilges,M. and Ehrlich,L.
StarDOM: From STAR Format to XML
J. Biomol. NMR (1999) 15, 169-172.

Elcock,A.H., Gabdoulline,R.R., Wade,R.C. and McCammon,J.A.
Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin
J. Mol. Biol. (1999) 291, 149-162.

Gabdoulline,R.R. and Wade,R.C.
On the Protein-Protein Diffusional Encounter Complex
J. Mol. Recogn. (1999) 12, 226-234.

Ibragimova,G. and Wade,R.C.
Stability of the beta-sheet of the WW domain: A Molecular Dynamics Simulation Study
Biophys. J. (1999) 77, 2191-2198.

Bitomsky,W. and Wade,R.C.
Docking of Glycosaminoglycans to Heparin-binding Proteins: Validation for aFGF, bFGF and Antithrombin and Application to IL-8
J. Am. Chem Soc. (1999), 121, 3004 – 3014.

Lounnas,V., Luedemann,S.K. and Wade,R.C.
Towards molecular dynamics simulations of large proteins with a hydration shell at constant presssure
Biophys. Chem. (1999) 78, 157-182.

Lamotte-Brasseur,J., Lounnas,V., Raquet,X. and Wade,R.C.
pKa calculations for class A beta-lactamases: influence of substrate binding.
Protein Sci (1999) 8, 404-409.

Nardi,F. and Wade,R.C.
Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations
In ”Molecular Dynamics: From Classical to Quantum Methods” Theoretical and Computational Chemistry Book Series, Vol. 7,
Eds. Balbuena,P.B. and Seminario,J.M.
Elsevier Science: Amsterdam, Netherlands (1999), Ch. 21, 859-898.

Knapp-Mohammady,M., Jalkanen,K.J., Nardi,F., Wade,R.C., Suhai,S.
L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence
of explicit water molecules and with continuum models using density functional theory

Chemical Physics (1999) 240, 63-77.

1998

Ringrose,L., Lounnas,V., Ehrlich,L., Buchholz,F., Wade,R.C., Stewart,F.A.
Comparative Kinetic Analysis of FLP and Cre Recombinases: Mathematical Models for DNA Binding and Recombination
Journal of Molecular Biology (1998) 284, 363-384.

Worth,G., Nardi,F. and Wade,R.C.
Use of Multiple Molecular Dynamics Trajectories to Study Biomolecules in Solution: The YTGP Peptide
J. Phys. Chem. (1998) 32, 6260-6272.

Wade,R.C., Gabdoulline,R.R., Luedemann,S.K. and Lounnas,V.
Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations
Proc. Natl. Acad. Sci. USA (1998) 95, 5942-5949, (and colloquium cover illustration).

Tomic,S., Gabdoulline,R.R., Kojic-Prodic,B. and Wade,R.C.
Classification of auxin related compounds based on similarity of their interaction fields: Extension to a new set of compounds
Internet J. Chem. (1998) 1, 26.

Ibragimova,G. and Wade,R.C.
Importance of explicit salt ions for protein stability in molecular dynamics simulation
Biophys. J. (1998) 74, 2906-2911.

Helms,V. and Wade,R.C.
Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy
J. Am. Chem. Soc. (1998) 120, 2710-2713.

Helms,V. and Wade,R.C.
The Hydration Energy Landscape of the Active Site Cavity in Cytochrome P450cam
Proteins (1998) 32, 381-396.

Gabdoulline,R.R. and Wade,R.C.
Brownian dynamics simulation of protein-protein diffusional encounter
In “Computer Simulations and Molecular Modeling Approaches to Biological Systems: Concepts and Applications”,
Methods (1998) 3, 329-341.

Wade,R.C., Gabdoulline,R.R. and Luty,B.A.
Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases
Proteins (1998) 31, 406-416, (and cover illustration).

Madura,J.D., Briggs,J.M., Wade,R.C. and Gabdoulline,R.R.
Brownian Dynamics
In “Encyclopedia of Computational Chemistry”
Eds. Schleyer,P.v.R., Allinger,N.L., Clark,T., Gasteiger,J., Kollman,P.A. and Schaefer,H.F., Schreiner,P.R.
John Wiley & Sons: Chichester, UK, (1998) 1, 141-154.

Tomic,S., Gabdoulline,R.R., Kojic-Prodic,B. and Wade,R.C.
Classification of auxin plant hormones by interaction property similarity indices
J. Comput. Aided Mol. Des. (1998) 12, 63-79.

Ehrlich,L., Reczko,M., Bohr,H. and Wade,R.C.
Prediction of protein hydration sites from sequence by modular neural networks
Protein Eng. (1998) 11, 11-19.

Wade,R.C., Ortiz,A.R. and Gago,F.
Comparative Binding Energy Analysis
In “3D QSAR in Drug Design. Volume 2: Ligand Protein Interactions and Molecular Similiarity” and
Perspectives in Drug Discovery and Design (1998) 9, 19-34.
Eds. Kubinyi,H., Folkers,G. and Martin,Y.
Kluwer Academic Publishers, Dordrecht, The Netherlands. (1998).

Wade,R.C. and Luedemann,S.
Computational strategies for modeling receptor flexibility in studies of receptor-ligand interactions
in “Experimental and Computational Approaches in Structure Based Drug Design”, Ed. P. W. Codding, NATO ASI Series, Kluwer, Dortrecht (1998) 41-52.

Wade,R.C., Sobolev,V., Ortiz,A.R. and Peters,G.
Computational approaches to modeling receptor flexibility upon ligand binding: Application to interfacially activated enzymes
in “Experimental and Computational Approaches in Structure Based Drug Design”, Ed. P. W. Codding, NATO ASI Series, Kluwer, Dortrecht (1998) 223-232.

1997

Wade,R.C.
‘Flu’ and Structure Based Drug Design
Structure (1997) 5, 1139-1146.

Raquet,X.,Lounnas,V., Lamotte-Brasseur,J., Frere,J.M. and Wade,R.C.
pKa Calculations for Class A Beta-lactamases: Methodological and Mechanistic Implications
Biophys. J. (1997) 73, 2416-2426.

Sobolev,V., Moallem,T.M., Wade,R.C., Vriend,G. and Edelman,M.
CASP2 molecular docking predictions with the LIGIN software
Proteins (1997) Suppl 1, 210-214.

Luedemann,S.K., Carugo,O. and Wade,R.C.
Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data
J. Mol. Model. (1997) 3, 369-374.

Nardi,F., Worth,G.A. and Wade,R.C.
Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis
Folding & Design (1997) 2, S62-68.

Lounnas,V. and Wade,R.C.
Exceptionally stable salt-bridges in cytochrome P450cam have functional roles
Biochemistry (1997) 36, 5402-5417.

Gabdoulline,R.R. and Wade,R.C.
Simulation of the Diffusional Association of Barnase and Barstar
Biophys. J. (1997) 72, 1917-1929, (and cover illustration).

Ortiz,A.R., Pastor, M., Palomer,A., Cruciani,G., Gago,F. and Wade,R.C.
Reliability of CoMFA Models:
Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors

J. Med. Chem. (1997) 40, 1136-1148, 4168.

Helms,V. and Wade,R.C.
Free energies of hydration from thermodynamic integration:
A comparison of molecular mechanics force fields and evaluation of calculations accuracy

J. Comp. Chem. (1997) 18, 449-462.

1996

Gabdoulline,R.R. and Wade,R.C.
Analytically defined surfaces to analyze molecular interaction properties
J. Mol. Graph. (1996) 14, 341-353.

Demchuk,E. and Wade,R.C.
Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins
J. Phys. Chem. (1996) 100, 17373-17387.

Wade,R.C. and Oschkinat,H.
Influence of glycosylation on the activity of rG-CSFs: in vitro studies: molecular structure and modeling
Intl. J. Hematology (1996) 64 Suppl. 2, S1-S2, S7-S8.

Schulze,H., Hui Bon Hoa,G., Helms,V., Wade,R.C. and Jung,C.
Structural Changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-Camphor and (1S)-Camphor
Biochemistry (1996) 35, 14127-14138.

Wade,R.C., Lounnas,V., Helms,V.,Hui Bon Hoa,G., Di Primo,C., Deprez,E., Barret,C., Kozin,S., Jung,C., Schulze,H., Contzen,J., Mouro,C., Gill,E., Simonneaux,G., Bondon,A., LeGrand,N. and Schlichting,I.
Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam
In “Perspectives on Protein Engineering” (Ed. M.J. Geisow), 3, BIODIGM, Nottingham (1996).

Worth,G.A., Lecuyer,C. and Wade,R.C.
TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations
J. Mol. Graph. (1996) 14, 173-182, 146-147.

Peters,G.H., Olsen,O.H., Svendsen,A. and Wade,R.C.
Theoretical investigation of the dynamics of the Active Site Lid in Rhizomucor Miehei Lipase
Biophys. J. (1996) 71, 119-129.

Reimer,N., Haenssgen,S., and Tichy,W.F.
Dynamically adapting the degree of parallelism with reflexive programs
In “Proceedings of the Third International Workshop on Parallel Algorithms for Irregularly Structure Problems”, Eds. Ferreira,A., Rolim,J., Saad,Y. and Yang, T., Springer, (1996) Lecture Notes in Computer Science, 1117, 313-318.

Sobolev,V., Wade,R.C., Vriend,G. and Edelman,M.
Molecular Docking Using Surface Complementarity
Proteins (1996) 25, 120-129.

Gabdoulline,R.R. and Wade,R.C.
Effective charges for Macromolecules in Solvent
J. Phys. Chem. (1996) 100, 3868-3878.

Helms,V., Deprez,E., Gill,E., Barret,C., Hui Bon Hoa,G. and Wade,R.C.
Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket
Biochemistry (1996) 35, 1485-1499.

Wade,R.C.
Brownian dynamics simulations of enzyme-substrate encounter
Biochem. Soc. Trans. (1996) 24, 254-259.

1995

Ortiz,A.R., Pisabarro,M.T., Gago,F. and Wade,R.C.
Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors
In “QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications”
Eds. Sanz,F., Giraldo,J., Manaut,F.
J.R. Prous Science Publishers, Barcelona, (1995) pp439-443.

Worth,G. and Wade,R.C.
The Aromatic – (i+2) Amine Interaction in Peptides
J. Phys. Chem. (1995) 99, 17473-17482.

Wade,R.C.
Simulation of enzyme-substrate interactions: the diffusional encounter step
Acta Bioch. Polon. (1995) 42, 419-425.

Worth,G. and Wade,R.C.
Molecular Dynamics Study of Short Peptide Sequences from BPTI displaying aromatic-amide interactions
AIP Conference Proceedings (1995) 330, 410.

Degenhardt,M. and Wade,R.C.
De novo design of ligands to block substrate access to cytochrome P450cam
J. Mol. Mod. (1995) 1, 93.

Madura,J.D., Briggs,J.M., Wade,R.C., Davis,M.E., Luty,B.A., Ilin,A., Antosiewicz,J., Gilson,M.K., Bagheri,B., Scott, L.R. and McCammon,J.A.
Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program
Comp. Phys. Comm. (1995) 91, 57-95.

Helms,V. and Wade,R.C.
Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study
Biophys. J. (1995) 69, 810-824.

Ortiz,A.R., Pisabarro,M.T., Gago,F. and Wade,R.C.
Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis
J. Med. Chem. (1995) 38, 2681-2691.

1994

Madura,J.D., Davis,M.E., Gilson,M.K., Wade,R.C., Luty,B.A. and McCammon,J.A.
Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations
Comp. Chem. Rev. (1994) 5, 229-267.

Pisabarro,M.T., Palomer,A., Ortiz,A.R., Wade,R.C., Gago,F., Mauleon,D. and Carganico,G.
Rational Drug Design: GRID- and LUDI-based Structural Modifications
of a Human Synovial Fluid Phospholipase A2 Inhibitor Leading to Enhanced Activity.

J. Mol. Graph. (1994) 12, 72.

Wade,R.C., Luty,B.A., Demchuk,E., Madura,J.D., Davis,M.E., Briggs,J.M. and McCammon,J.A.
Simulation of Enzyme-Substrate Encounter with Gated Active Sites
Nature Struct. Biol. (1994) 1, 65-69.

Pisabarro,M.T., Ortiz,A.R., Palomer,A., Cabre,F., Garcia,L., Wade,R.C., Gago,F., Mauleon,D. and Carganico,G.
Rational Modification of Human Synovial Fluid Phospholipase A2 Inhibitors
J. Med. Chem. (1994) 37, 337-341.

Demchuk,E., Mueller,T., Oschkinat,H., Sebald, W. and Wade,R.C.
Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis
Protein Science (1994) 3, 920-935, (and cover illustration).

Pisabarro,M.T., Ortiz,A.R., Serrano,L. and Wade,R.C.
Homology Modeling of the Abl-SH3 domain
Proteins (1994) 20, 203-215.

1993

Luty,B.A., Wade,R.C., Madura,J.D., Davis,M.E., Briggs,J.M. and McCammon,J.A.
Brownian Dynamics Simulations of Diffusional Encounters between Triose Phosphate Isomerase
and Glyceraldhyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate

J. Phys. Chem. (1993) 97, 233-237.

Wade,R.C., Davis,M.E., Luty,B.A., Madura,J.D. and McCammon,J.A.
Gating of the Active Site of Triose Phosphate Isomerase:
Brownian Dynamics Simulations of Flexible Peptide Loops in the Enzyme

Biophys. J. (1993) 64, 9-15.

Wade,R.C., Clark,K. and Goodford,P.J.
Further Development of Hydrogen-Bond Functions for Use in Determining
Energetically Favorable Binding Sites on Molecules of Known Structure.
1. Ligand Probe Groups with the Ability To Form Two Hydrogen Bonds

J. Med. Chem. (1993) 36, 140-147.

Wade,R.C. and Goodford,P.J.
Further Development of Hydrogen-Bond Functions for Use in Determining
Energetically Favorable Binding Sites on Molecules of Known Structure.
2. Ligand Probe Groups with the Ability To Form More Than Two Hydrogen Bonds

J. Med. Chem. (1993) 36, 148-156.

Demchuk,E., Vihinen,M., Wade,R. and Korpela,T.
Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase.
In “Stability and Stabilization of Enzymes”
Eds. van der Tweel,W.J.J., Harder,A. and Buitelaar,R.M.
Elsevier, Netherlands. (1993) pp291-298.

Wade,R.C., Bohr,H. and Wolynes,P.G.
Use of neural networks to predict hydration sites in proteins.
In “Trends in QSAR and Molecular Modelling ’92”
Ed. Wermuth,C.G.
ESCOM, Leiden, (1993) pp396-397.

Wade,R.C.
Molecular Interaction Fields.
In “3D QSAR in Drug Design. Theory, Methods and Applications”
Ed. Kubinyi,H.
ESCOM, Leiden, (1993), pp486-505.

1992

Wade,R.C. and McCammon,J.A.
Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus.
Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations.
I Mapping the Rotamers of Residue 188 of Viral Protein 1

J. Mol. Biol. (1992) 225, 679-696.

Wade,R.C. and McCammon,J.A.
Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus.
Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations.
II. Calculations of Free-energy Differences by Thermodynamic Integration

J. Mol. Biol., (1992) 225, 697-712.

Wade,R.C., Bohr,H. and Wolynes,P.G.
Prediction of Water Binding Sites on Proteins by Neural Networks
J. Am. Chem. Soc. (1992), 114, 8284-8285.
1991
Wade,R.C., Mazor,M.H., McCammon,J.A. and Quiocho,F.A.
A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins.
Biopolymers (1991) 31, 919-931.

1990
Wade,R.C.
An Approach to the Design of Anti-Influenza Agents
In “Use of X-Ray Crystallography in the Design of Antiviral Agents”
Eds. Laver,G. and Air,G.
Academic Press, Inc., San Diego (1990) pp61-74.

Wade,R.C.
Solvation of the Active Site of Cytochrome P450-cam.
J. Comp. Aided Mol. Des. (1990) 4, 199-204.

Wade,R.C., Mazor,M.H., McCammon,J.A. and Quiocho,F.A.
Hydration of Cavities in Proteins: a Molecular Dynamics Approach.
J. Am. Chem. Soc. (1990) 112, 7057-7059.

1989

Wade,R.C. and Goodford,P.J.
The Role of Hydrogen-bonds in Drug Binding
In “Computer-assisted Modeling of Receptor-Ligand Interactions. Theoretical Aspects and Applications to Drug Design”
Ed. Golombek,A., Alan R. Liss, Inc. New York
Prog. Clin. Biol. Res. (1989) 289, pp433-444.

Boobbyer,D.N.A., Goodford,P.J., McWhinnie,P.M. and Wade,R.C.
New Hydrogen-bond Potentials for Use in Determining Energetically Favourable Binding Sites on Molecules of Known Structure.
J. Med. Chem. (1989) 32, 1083-1094.

Reynolds,C.A., Wade,R.C. and Goodford,P.J.
Identifying Targets for Bioreductive Agents
J. Mol. Graph. (1989) 7, 103-108.

1988

Wade,R.C. and Goodford,P.J.
The Use of Molecular Graphics in the Design of Anti-influenza Agents
Br. J. Pharmac. Proc. Suppl. (1988) 95, 588P.

Wade,R.C
Ligand-Macromolecule Interactions
D.Phil. Thesis, University of Oxford (1988).

2011-present

2016

Musa Ozboyaci.
Modeling and Simulation of Protein-Surface Interactions.
Ph.D. Thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany (HITS).

Astrid Stubbusch.
Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).

2015

Michael Berinski.
Macromolecular Interactions: in silico prediction of the structures of complexes between proteins.
Ph.D. Thesis, Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany (HITS).

Max Horn.
Clustering and Scoring the Druggability of Transient Protein Pockets.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).

Max Waldhauer.
Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).

Gaurav Kumar Ganotra.
Methods to Compute and Investigate Drug Binding Kinetics.
Master’s Thesis, Life Science Informatics, University of Bonn, Germany. (HITS).

Xiaofeng Yu.
Multiscale Simulations of Cytochrome P450 Systems.
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany. (HITS).

2014

Rudi Tong.
Comparative analysis of Adenylyl Cyclase binding sites.
Bachelor’s thesis, Molecular Biotechnology, Faculty of Biosciences Ruprecht-Karls University, Heidelberg, Germany. (HITS).

2013

Priyanka Banerjee.
An Algorithmic Approach to Peptidomimetics.
Master’s thesis, Masters Programme in Life Science Informatics Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Germany. (HITS).

2012

Thomas Monninger.
Dynamische hybride Cloud für wissenschaftliche Anwendungen.
Master’s thesis, Fakultaet fuer Mathematik und Informatik Ruprecht-Karls University, Heidelberg, Germany. (HITS).

2011

Sundar Raman Subramaniam.
Sequence, Structure and Stability of Collagen and its Interaction with Collagenase.
PhD thesis, University of Madras, Chennai., India. (Visiting Ph. D. Student (DAAD Sandwich Scholar) to HITS from Central Leather Research Institute (CLRI)).

Divita Garg.
Computational and NMR Studies of Thymidylate Synthase and its Regulation., (2011)
PhD thesis, Faculty of Chemistry, Technical University of Munich, Germany. (HITS), (TUM) .

Nadine Veith.
Structural Comparison of Pyruvate Kinases.
Master’s thesis, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, Germany. (HITS).

Erika Nerini.
System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action., (2011)
PhD thesis, Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia, Italy. (Visiting Phd Student to HITS from University of Modena).

2002-2010

2010

Anna Feldman-Salit.
Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex., (2010)
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany. (HITS).

2009

Georgi V. Pachov.
Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study., (2009)
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg, Germany. (HITS).

Mykhaylo Berynskyy.
Automatisierte Analyse von Brownian Dynamics Simulationen.
Master’s thesis, Bioinformatics, Giessen-Friedberg University of Applied Sciences, Germany. (HITS).

2007

Domantas Motiejunas.
Modeling of macromolecular interactions.
PhD thesis, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg, Germany. (HITS).

2006

Mai Zahran.
Analyse a haut debit des proprietes electrostatiques des proteines de la famille des ubiquitines (High-throughput analysis of the electrostatic properties of proteins of the ubiquitin family). , (2006)
Master’s thesis, Bioinformatics, University Paris VII, France. (HITS).

2005

Tim I. Johann.
Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models., (2005)
Diplom thesis, Physics, Ruperto-Carola University,Heidelberg, Germany. (HITS).

Stefan Ulbrich.
The Protein Structure Annotation Tool ProSAT2.
Studienarbeit, Computer Science, University of Karlsruhe, Germany . (HITS).

Bruno Besson.
Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications. , (2005)
Master’s thesis, Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon, France. (HITS).

2004

Domantas Motiejunas.
Protein-protein docking assisted by sequence conservation and experimental data., (2004)
Master’s thesis, Molecular Biology, Ruperto-Carola University,Heidelberg, Germany. (HITS).

Henrik R.Hallingbaeck.
Peroxidases: A computational study of ligand binding and enzyme kinetics., (2004)
Master’s thesis, Molecular Biotechnology, Uppsala University School of Engineering, Uppsala, Sweden. (HITS).

2003

Gunter F. Neumann.
Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem., (2003)
Diplom thesis, Physics, Ruperto-Carola University,Heidelberg, Germany. (EML).

Octave M. Noubibou Doudieu.
Using Sequence Information in Protein Docking Procedures.
Master’s thesis, Bioinformatics, University of Applied Sciences Berlin, Germany. (EML).

James N.D. Battey.
High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes., (2003)
Master’s thesis, Bioinformatics, Exeter University, Exeter, United Kingdom. (EMBL).

Lakshmi V. Padmavathi Pulagam.
Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway., (2003)
Master’s thesis, Bioinformatics, Cologne University Bioinformatics Center, University of Cologne, Germany. (EMBL).

1995-2001

2001

Aitor Gonzalez.
Glycolytic Pathway Reaction Animations.
Diplom thesis, Biology, Ruperto-Carola University,Heidelberg Germany. (EML/EMBL).

Stefania Ferrari.
Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase. , (2001)
PhD thesis, University of Modena and Reggio Emilia, Modena, Italy, . (Visiting Ph.D. student to EMBL from University of Modena).

1999

Frederico Nardi.
Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues. , (1999)
PhD thesis, Universite Joseph Fourier, Grenoble, France. (EMBL).

Francesca De Rienzo.
Computational studies of blue copper proteins.
PhD thesis, University of Modena and Reggio Emilia, Modena, Italy . (Visiting Ph.D. student to EMBL from University of Modena).

Masakazu Koboyashi.
Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics. , (1999)
Master’s thesis, University of York, United Kingdom. (EMBL).

Ralph Gauges.
Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF., (1999)
Diplom thesis, Biology, Eberhard-Karls University, Tubingen, Germany, . (EMBL).

1998

Wolfgang Bitomsky.
Binding of Glycosaminoglycans to Heparin-Binding Proteins.
PhD thesis, University of Vienna, Austria. (Visiting Ph.D. student to EMBL from University of Vienna).

1996

Niels Reimer.
Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen., (1996)
Diplom thesis, Computer Science, University of Karlsruhe, Tubingen, Germany. (EMBL).

Angel Ramirez Ortiz.
Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships. , (1996)
PhD thesis, University of Alcala de Henares, Madrid, Spain. (EMBL).

Volkhard Helms.
Hydratation des aktiven Zentrums von Cytochrom P450cam – Untersuchung mit Molekueldynamik-Simulationen., (1996)
PhD thesis, Ludwig-Maximilians University, Munich, Germany. (EMBL).

1995

Michael Degenhardt.
De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam., (1995)
Diplom thesis, Biology, Ruperto-Carola University, Heidelberg, Germany. (EMBL).

Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg
A Quick Guide for Building a Successful Bioinformatics Community.
PLoS Comput Biol., (2015) 11(2):e1003972. (Fulltext).

Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood.
Ten Simple Rules for Organizing an Unconference.
PLoS Comput Biol., (2015) 11(1):e1003905. (Fulltext).

Jonathan C. Fuller, Pierre Khoueiry, Holger Dinkel, Kristoffer Forslund, Alexandros Stamatakis, Joseph Barry, Aidan Budd, Theodoros G. Soldatos, Katja Linssen, Abdul Mateen Rajput
Biggest challenges in bioinformatics.
EMBO reports. (2013) 14:302-4. (Abstract).

Wade, R.C.
Das biomolekulare Erkennungspuzzle.
Spektrum der Wissenschaft Extra (2011) 2, 14-17 (Fulltext).

“Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer” United States Patent No.: US 8,916,679 B2, Date of Patent: 23.12.2014. Filed: 17.08.2012, 01.12.2009; Costi MP, Marverti G, Cardinale D, Venturelli A, Ferrari S, Ponterini G (Univ. Modena), Henrich S, Salo-Ahen O, Wade R. (HITS).

“Uso di inhibitori della Pteridina Reduttasi per la prevenzione e/o il trattamento di infezioni parassitarie”, Italian Patent Nr. 1403584, Date of Patent: 31.10.2013, Filed : 25.11.2010; Costi MP, Luciani R, Nerini E, Guerrieri D, Ferrari S, Venturelli A, Lazzari S, (Univ. Modena); Wade R, Henrich S, Motiejunas D. (HITS).