Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields| Mol. BioSyst., 2009, in press. Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
Computational approaches to identifying and characterizing protein binding sites for ligand design| Proteins, 2009, in press. Stefan Henrich, Isabella Feierberg, Ting Wang, Niklas Blomberg and Rebecca C. Wade (Abstract)
Comparative binding energy analysis for binding affinity and target selectivity prediction | J. Mol. Recogn, 2009, in press. Stefan Henrich, Outi M.H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani and Rebecca C. Wade (Abstract)
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate|Nature Chem. Biol., 2009, in press. Martina Pavlova, Martin Klvana, Zbynek Prokop, Radka Chaloupkova, Pavel Banas, Michal Otyepka, Rebecca C. Wade, Masataka Tsuda, Yuji Nagata and Jiri Damborsky (Abstract)
Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.|J. Mol. Biol., 2009, in press. 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 (Abstract)
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. Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
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, pp 109-128. Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
A mechanistic model of the cysteine synthase complex.| J. Mol. Biol., 2009, 386, 37-59. Anna Feldman-Salit, Markus Wirtz, Rüdiger Hell and Rebecca C. Wade (Abstract)
Molecular Recognition, Computation and Modeling of.| Wiley Encyclopedia of Chemical Biology, John Wiley and Sons, Inc, 2009, doi:10.1002/9780470048672.wecb354. Anna Feldman-Salit and Rebecca C. Wade (Abstract)
2008:
webPIPSA: a web server for the comparison of protein interaction properties | Nucl. Acids Res. (2008) 36, W276-280. Stefan Richter, Anne Wenzel, Matthias Stein,Razif R. Gabdoulline, Rebecca C. Wade (Abstract)(webPIPSA website)
SYCAMORE - a systems biology computational analysis and modeling research environment | Bioinformatics (2008) 24, 1463-1464.
Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline, Irina Surovtsova, Niels Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade, Ursula Kummer (Abstract)(SYCAMORE website)
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.
Heidrun Witan, Andreas Kern, Ingrid Koziollek-Drechsler, Rebecca Wade, Christian Behl, and Albrecht M. Clement
(Abstract)
Protein-protein docking by simulating the process of association subject to biochemical constraints. | Proteins (2008) 71, 1955-1969. Domantas Motiejunas, Razif R. Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade (Abstract)
Calculating Enzyme Kinetic Parameters from Protein Structures | Biochem. Soc. Trans. (2008) 36, 51-54. Matthias Stein,Razif R. Gabdoulline, Rebecca C. Wade (related Poster Abstract)
On the Use of PIPSA to guide target-selective drug design | ChemMedChem (2008) i3, 413-417. (Link) Stefan Henrich, Stefan Richter, Rebecca C. Wade
Mechanism of auxin interaction with auxin binding protein (ABP1): a molecular dynamics simulation study | Biophys. J. (2008) 94, 27-37.
Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade, Sanja Tomic (Abstract) (Journal Cover)
2007:
qPIPSA: Relating enzymatic kinetic parameters and interaction fields | BMC Bioinformatics (2007) 8, 373. Razif R. Gabdoulline, Matthias Stein, Rebecca C. Wade (Fulltext)
Bridging from molecular simulation to biochemical networks | Curr. Op. Struct. Biol. (2007) 17, 166-172. Matthias Stein,Razif R. Gabdoulline, Rebecca C. Wade (Abstract)
Exploring Biomolecular Recognition by Modelling and Simulation | In In "Modelling and Simulation in Science. Proceedings of the 6th International Workshop on Data Analysis in Astronomy "Livio Scarsi" ", V. Di Gesu, G. Lo Bosco, M.C. Maccarone (Eds.) World Scientific Publishing Co. (2007) 150-153. 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 (2007) 36, 69-74. Georgi Pachov, Razif R. Gabdoulline, Rebecca C. Wade (Fulltext)
On the Use of Elevated Temperature in Simulations to Study Protein Unfolding Mechanisms.
| J. Chem. Theory Comput. (2007) 3, 1476-1483.
Ting Wang and Rebecca C. Wade (Abstract)
Structural and electrostatic properties of ubiquitination and related pathways | Frontiers in Bioscience (2007) 12, 3419-3430. Peter J. Winn, Mai Zahran, James N.D. Battey, Yanxiang Zhou, Rebecca C. Wade, Amit Banerjee (Abstract) (Figures)
COMBINE Analysis of the Specificity of Binding of Ras Proteins to their Effectors | Proteins (2007) 67, 435-447.
Sanja Tomic, Branimir Bertosa, Ting Wang, Rebecca C. Wade (Abstract)
Comparisons of the Protein Electrostatic Potentials as a Means to Understanding Function. | In "Protein Folding and Drug Design. Proceedings of the International School of Physics "Enrico Fermi" ", R.A: Broglia, L. Serrano, G.Tiana (Eds.) Societa Italiana di Fisica, Bologna, Italy (2007) 165, 207-219.
Peter J .Winn, Mai Zahran, Rebecca C. Wade
FTIR studies of the redox partner interaction in cytochrome P450. The Pdx-P450cam couple.
| Biochimica et Biophysica Acta. General Subjects (2007) 1770, 420-431. Andrey Karyakin, Domantas Motiejunas, Rebecca C. Wade, Christiane Jung (Abstract)
The Estimation of Kinetic Parameters in Systems Biology by Comparing
Molecular Interaction Fields of Enzymes | Beilstein Proceedings of the
2nd Conference on Experimental Standard Conditions of Enzyme
Characterizations, 19-23 March, 2006, Ruedesheim, 2007, 237-253.(Fulltext) Matthias Stein, Razif R. Gabdoulline, Bruno Besson, Rebecca C. Wade.
The Ins and Outs of Cytochrome P450s.
| Biochimica et Biophysica Acta. General Subjects (2007) 1770, 390-401.
Vlad Cojocaru, Peter J. Winn, Rebecca C. Wade (Abstract)
Structural, Energetic, and Dynamic Aspects
of Ligand–Receptor Interactions |
Comprehensive Medicinal Chemistry II, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford, 2007 (ISBN
0080445136), Vol. 4, 193-213.
Domantas Motiejunas and Rebecca C. Wade.
Characterization of Protein-Binding Sites and Ligands Using Molecular Interaction Fields|
Comprehensive Medicinal Chemistry II, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford, 2007 (ISBN
0080445136), Vol. 4, 237-253.
Gabriele Cruciani, Emanuele Carosati, Rebecca C. Wade and Massimo Baroni.
2006:
Integrating Structural and Kinetic Enzymatic
Information in Systems Biology. | NIC Workshop 2006 'From Computational Biophysics to
Systems Biology', 6-9 June, John von Neumann Institute for Computing, Juelich | NIC Series (2006) 34, 129-132. Matthias Stein, Razif R. Gabdoulline,Rebecca C. Wade (Abstract & Full text)
Molecular Docking. | Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, Ed. Ganten,D. and Ruckpaul, K., Springer (2006) pp1149-1153.
Karin Schleinkofer, Ting Wang, Rebecca C. Wade
ProSAT2-Protein Structure Annotation Server
| Nucl. Acids. Res. (2006) 34, W79-W83.
Razif R. Gabdoulline, Stefan Ulbrich, Stefan Richter and Rebecca C. Wade(Abstract & Full text)(Webserver)
Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking.
| Biochemistry (2006) 45, 2940-2950.
Henrik R. Hallingbaeck, Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
Diffusional encounter of barnase and barstar.
| Biophys. J. (2006) 90, 1913-1924.
Alexander Spaar, Christian Dammer, Razif R. Gabdoulline, Rebecca C. Wade and Volkhard Helms (Abstract)
Force Field Effects on a beta-sheet Protein Domain Structure in Thermal Unfolding Simulations.
| J. Chem. Theory Comput. (2006) 2, 140-148.
Ting Wang and Rebecca C. Wade (Abstract)
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.
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 (Abstract)
2005:
Multiple molecular recognition mechanisms. Cytochrome P450—A case study.
| Biochimica et Biophysica Acta. (2005) 1754, 239-244. Rebecca
C. Wade, Domantas Motiejunas, Karin Schleinkofer, Sudarko, Peter J.
Winn, Amit Banerjee, Andrei Kariakin and Christiane Jung (Abstract)
Calculation and Application of Molecular Interaction Fields.|
In ‘Molecular Interaction Fields. Applications in Drug Discovery and
ADME Prediction’, Ed. Cruciani, G., Wiley-VCH, Weinheim.
(ISBN 3-527-31087-8) (2005)Ch. 2, pp27-42. Rebecca C. Wade (Publisher link)
Pushing the limits: Editorial overview. | Curr. Opin. Struct. Biol. (2005)15, 135-136. J. Andrew McCammon and Rebecca C. Wade (Link)
Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?| EMBO Reports (2005)6, 584-589. Karin Schleinkofer, Sudarko, Peter J. Winn, Susanna K. Lüdemann and Rebecca C. Wade (Abstract)
Recognition Highlights and Commentaries | J. Mol. Recognit. (2005)18, 191. Rebecca C. Wade (Link)
Quantitative Analysis
of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas
paucimobilis UT26.| Biochemistry (2005) 44, 3390-3401. Jan Kmunicek, Kamila Hynkova, Tomas Jedlicka, Yuji Nagata, Ana Negri, Federico Gago, Rebecca C. Wade and Jiri Damborsky (Abstract)
Issues in High-Throughput
Comparative Modelling: A Case Study Using the Ubiquitin E2 Conjugating Enzymes.| Proteins (2005)58, 367-375. Peter J. Winn, James N. Battey, Karin Schleinkofer, Amit Banerjee and Rebecca C. Wade (Abstract)
The Impact of Protein Flexibility on Protein-protein Docking.| Proteins (2005)58, 126-133. Lutz P. Ehrlich, Michael Nilges and Rebecca C. Wade (Abstract)
2004:
Using 3D protein structures to derive 3D-QSARs
| Drug Discovery Today: Technologies (2004) 1(3), 241-246. Rebecca C. Wade, Stefan Henrich and Ting Wang (Abstract)
Comparative Structural and Energetic Analysis of WW Domain-Peptide
Interactions| J. Mol. Biol. (2004) 344, 865-881. Karin Schleinkofer, Urs Wiedemann, Livia Otte, Ting Wang, Gerd
Krause, Hartmut Oschkinat and Rebecca C. Wade (Abstract)
Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family.| Structure (2004) 12, 1563-74. Peter J. Winn, Tomasz L. Religa, James D. Battey, Amit Banerjee and Rebecca C. Wade (Abstract)The Ubiquitin and Ubiquitin-like Protein Web Resource
How Optimal are the Binding Energetics of Barnase and Barstar? | Biophys. J. (2004) 12, 1563-74. Ting Wang, Sanja Tomic, Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins | Cell Mol. Life Sci (2004) 61, 1123-1142. Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade, Marco Sola and M Cristina Menziani (Abstract)
A survey of active site access channels in cytochromes P450 | J. Inorg. Biochem. (2004) 98, 1175-1182. Rebecca C. Wade, Peter J. Winn, Ilme Schlichting and Sudarko (Abstract)
Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis |
In "Enzyme functionality: Design, Engineering and Screening", Ed. A.
Svendsen, Marcel Dekker, New York, ISBN: 0-8247-4709-7 (2004) pp79-96. Jiri Damborsky, Jan Kmunicek, Tomas Jedlicka,Santos Luengo, Federico Gago, Angel R. Ortiz and Rebecca C. Wade
2003:
In Search of the Prototype of Nitric Oxide Synthase | FEBS Letts. (2003) 554, 1-5. Tomasz Zemojtel, Rebecca C. Wade and Thomas Dandekar (Abstract)
Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase | Chemistry & Biology (2003) 10, 1183-1193. Stefania Ferrari, M. Paola Costi and Rebecca C. Wade (Abstract)
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 | J. Chem. Inf. Comput. Sci.(2003) 43, 1532-1541. Branimir
Bertosa, Biserka Kojic-Prodic,Rebecca C. Wade, Michael Ramek, Stavroula
Piperaki, Anna Tsantili-Kakoulidou and Sanja Tomic (Abstract)
What Determines the Redox Potential of Ferredoxins? | In "Proceedings of the 13th International Conference on Cytochromes P450", Monduzzi Editore, Bologna.(2003), pp25-30. Timm Essigke, G. Matthias Ullmann and Rebecca C. Wade
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. Jan Kmunicek, Michal Bohac, Santos Luengo, Federico Gago, Rebecca C. Wade and Jiri Damborsky (Abstract)
MolSurfer: a macromolecular interface navigator | Nucleic Acids Res. (2003), 31, 3349-3351. Razif Gabdoulline, Rebecca C. Wade and Dirk Walther (Abstract)(Fulltext)(Webserver)
Concerted Simulations Reveal How Peroxidase Compound III Formation Results in Cellular Oscillations | Biophys. J. (2003), 85, 1421-1428. Razif Gabdoulline, Ursula Kummer, Lars F. Olsen and Rebecca C. Wade (Abstract)(Fulltext)(Movie)
ProSAT: Functional annotation of protein 3D structures | Bioinformatics (2003), 19, 1723-1725. Razif Gabdoulline, Rene Hoffmann, Florian Leitner and Rebecca C. Wade (Abstract)(Webserver)
DSMM - a Database of Simulated Molecular Motions | Nucleic Acids Res. (2003), 31, 456-457. Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez and Rebecca C. Wade (Abstract)(Fulltext)(Database)
Implicit Solvent Models for Flexible Protein-protein Docking by Molecular Dynamics Simulation | Proteins (2003), 50, 158-169. Ting Wang and Rebecca C. Wade (Abstract)
2002:
Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytocromes P450cam and P450lin | J. Inorg. Biochem. (2002), 91, 597-606. Eric Deprez, Edward Gill, Volkhard Helms, Rebecca C. Wade and Gaston Hui Bon Hoa (Abstract)
Comparative Binding Energy (COMBINE) Analysis of OppA-peptide Complexes | J. Med. Chem. (2002), 45, 4828-4837. Ting Wang and Rebecca C. Wade (Abstract)
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. Peter J. Winn, Susanna K. Lüdemann, Ralph Gauges, Valere Lounnas and Rebecca C. Wade (Abstract)(Full text)
Biomolecular diffusional association | Curr. Opin. Struct. Biol., (2002), 12, 204-213. Razif R. Gabdoulline and Rebecca C. Wade (Abstract)
Elusive recognition determinants for ubiquitination | J. Molec. Recogn. (2002) 15, 3-5 Amit Banerjee and Rebecca C. Wade (Abstract)
Biologically
relevant properties of copper-containing proteins analysed by means of
semi-quantitative and quantitative theoretical descriptors | Handbook of Copper Pharmacology and Toxicology, Ed. E. J. Massaro, Humana Press, Totowa, New Jersey (2002) pp. 53-80. Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade, M. Cristina Menziani
