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MCM Group - Publications

2010

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. in press.

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.

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.

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.

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.

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

S. Richter, A. Wenzel, M. Stein, R. R. Gabdoulline and R. 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. (related Poster 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) , (related Poster 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.

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.

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), (Figures).

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.

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 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. (Abstract) ; (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.

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.