• Protein-protein docking by simulating the process of association subject to biochemical constraints. | Proteins (2008) accepted.
  Domantas Motiejunas, Razif R. Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade
  
• Molecular Recognition, Computation and Modeling of.| Encyclopedia of Chemical Biology, Wiley, 2008, accepted.
  Anna Feldman-Salit and 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)

• On the Use of PIPSA to guide target-selective drug design | ChemMedChem (2007) 2, 1-5 (Link)
  Stefan Henrich, Stefan Richter, Rebecca C. Wade
  
• 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)
• Calculating Enzyme Kinetic Parameters from Protein Structures | Biochem. Soc. Trans. (2007).
  Matthias Stein,Razif R. Gabdoulline, Rebecca C. Wade 
• Exploring Biomolecular Recognition by Modelling and Simulation | In Proceedings of the 6th International Workshop on 'Data Analysis in Astronomy "Livio Scarsi" "Modelling and Simulation in Science" ' Biophys. Rev. Lett. (2007).
  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. | Proceedings of the International School of Physics "Enrico Fermi" Workshop on Protein Folding and Drug Design (2007) in press.
  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.

• 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)

• 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)

• 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