Solvation of the active site of cytochrome P450-cam. - Rebecca C. Wade (J. Comput. Aided Mol. Des., 1990)

Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. - Volkhard Helms; Rebecca C. Wade (J. Comput. Chem., 1997)

Classification of auxin plant hormones by interaction property similarity indices. - Sanja Tomic; Razif R. Gabdoulline; Biserka Kojic-Prodic; Rebecca C. Wade (J. Comput. Aided Mol. Des., 1998)

3D modeling of macromolecular structures and reactions in the context of genomes. - Razif R. Gabdoulline; Aitor González; Rebecca C. Wade (German Conference on Bioinformatics, 2001)

ProSAT: functional annotation of protein 3D structures. - Razif R. Gabdoulline; René Hoffmann; Florian Leitner; Rebecca C. Wade (Bioinform., 2003)

Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. - Jan Kmunícek; Michal Bohác; Santos Luengo; Federico Gago; Rebecca C. Wade; Jirí Damborský (J. Comput. Aided Mol. Des., 2003)

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. - Branimir Bertosa; Biserka Kojic-Prodic; Rebecca C. Wade; Michael Ramek; Stavroula Piperaki; Anna Tsantili-Kakoulidou; Sanja Tomic (J. Chem. Inf. Comput. Sci., 2003)

DSMM: a Database of Simulated Molecular Motions. - Giacomo Finocchiaro; Ting Wang; René Hoffmann; Aitor González; Rebecca C. Wade (Nucleic Acids Res., 2003)

MolSurfer: a macromolecular interface navigator. - Razif R. Gabdoulline; Rebecca C. Wade; Dirk Walther 001 (Nucleic Acids Res., 2003)

ProSAT2 - Protein Structure Annotation Server. - Razif R. Gabdoulline; S. Ulbrich; Stefan Richter 002; Rebecca C. Wade (Nucleic Acids Res., 2006)

qPIPSA: Relating enzymatic kinetic parameters and interaction fields. - Razif R. Gabdoulline; Matthias Stein; Rebecca C. Wade (BMC Bioinform., 2007)

SYCAMORE - a systems biology computational analysis and modeling research environment. - Andreas Weidemann; Stefan Richter 002; Matthias Stein; Sven Sahle; Ralph Gauges; Razif R. Gabdoulline; Irina Surovtsova; Nils Semmelrock; Bruno Besson; Isabel Rojas; Rebecca C. Wade; Ursula Kummer (Bioinform., 2008)

webPIPSA: a web server for the comparison of protein interaction properties. - Stefan Richter 002; Anne Wenzel; Matthias Stein; Razif R. Gabdoulline; Rebecca C. Wade (Nucleic Acids Res., 2008)

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

Targeting protein dynamics in drug design. - Rebecca C. Wade (J. Cheminformatics, 2013)

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins. - Daria B. Kokh; Stefan Richter 002; Stefan Henrich; Paul Czodrowski; Friedrich Rippmann; Rebecca C. Wade (J. Chem. Inf. Model., 2013)

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

LigDig: a web server for querying ligand-protein interactions. - Jonathan C. Fuller; Michael Martinez; Stefan Henrich; Antonia Stank; Stefan Richter 002; Rebecca C. Wade (Bioinform., 2015)

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. - Michael Martinez; Neil J. Bruce; Julia Romanowska; Daria B. Kokh; Musa Ozboyaci; Xiaofeng Yu; Mehmet Ali Öztürk; Stefan Richter 002; Rebecca C. Wade (J. Comput. Chem., 2015)

webSDA: a web server to simulate macromolecular diffusional association. - Xiaofeng Yu; Michael Martinez; Annika L. Gable; Jonathan C. Fuller; Neil J. Bruce; Stefan Richter 002; Rebecca C. Wade (Nucleic Acids Res., 2015)

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. - 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; et al. (Nat., 2015)

Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. - Wiktoria Jedwabny; Joanna Panecka-Hofman; Edyta Dyguda-Kazimierowicz; Rebecca C. Wade; W. Andrzej Sokalski (J. Comput. Aided Mol. Des., 2017)

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. - Antonia Stank; Daria B. Kokh; Max Horn; Elena Sizikova; Rebecca Neil; Joanna Panecka; Stefan Richter 002; Rebecca C. Wade (Nucleic Acids Res., 2017)

KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding. - Neil J. Bruce; Gaurav K. Ganotra; Stefan Richter 002; Rebecca C. Wade (J. Chem. Inf. Model., 2019)

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. - Neil J. Bruce; Daniele Narzi; Daniel Trpevski; Siri Camee van Keulen; Anu G. Nair; Ursula Rothlisberger; Rebecca C. Wade; Paolo Carloni; Jeanette Hellgren Kotaleski (PLoS Comput. Biol., 2019)

Druggability Assessment in TRAPP Using Machine Learning Approaches. - Jui-Hung Yuan; Sungho Bosco Han; Stefan Richter 002; Rebecca C. Wade; Daria B. Kokh (J. Chem. Inf. Model., 2020)

Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. - Ariane Nunes-Alves; Fabian Ormersbach; Rebecca C. Wade (J. Chem. Inf. Model., 2021)

Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. - Lucas G. Viviani; Daria B. Kokh; Rebecca C. Wade; Antonia T. do Amaral (J. Chem. Inf. Model., 2023)

EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. - Ganna Gryn'ova; Tristan Bereau; Carolin Müller; Pascal Friederich; Rebecca C. Wade; Ariane Nunes-Alves; Thereza A. Soares; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2024)

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning. - Matheus Vf Ferraz; W. Camilla S. Adan; Tayná E. Lima; Adriele J. C. Santos; Sérgio O. de Paula; Rafael Dhalia; Gabriel da Luz Wallau; Rebecca C. Wade; Isabelle F. T. Viana; Roberto D. Lins (PLoS Comput. Biol., 2025)