Rebecca C. Wade

31 papers Journal 30Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Multiscale Simulation Approach to Compute Protein-Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics. J. Chem. Inf. Model. Abraham Muñiz-Chicharro, Gaurav K. Ganotra, Rebecca C. Wade
2025	J	`jnl`	Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning. PLoS Comput. Biol. Matheus Vitor Ferreira 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
2024	J	`jnl`	EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. J. Chem. Inf. Model. Ganna Gryn'ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth M. Merz Jr.
2023	J	`jnl`	Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. J. Chem. Inf. Model. Lucas G. Viviani, Daria B. Kokh, Rebecca C. Wade, Antonia T. do Amaral
2021	J	`jnl`	Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. J. Chem. Inf. Model. Ariane Nunes-Alves, Fabian Ormersbach, Rebecca C. Wade
2020	J	`jnl`	Druggability Assessment in TRAPP Using Machine Learning Approaches. J. Chem. Inf. Model. Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade, Daria B. Kokh
2019	J	`jnl`	KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding. J. Chem. Inf. Model. Neil J. Bruce, Gaurav K. Ganotra, Stefan Richter, Rebecca C. Wade
2019	J	`jnl`	Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. PLoS Comput. Biol. Neil J. Bruce, Daniele Narzi, Daniel Trpevski, Siri Camee van Keulen, Anu G. Nair, Ursula Rothlisberger, Rebecca C. Wade, Paolo Carloni, Jeanette Hellgren Kotaleski
2017	J	`jnl`	Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. J. Comput. Aided Mol. Des. Wiktoria Jedwabny, Joanna Panecka-Hofman, Edyta Dyguda-Kazimierowicz, Rebecca C. Wade, W. Andrzej Sokalski
2017	J	`jnl`	TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Res. Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade
2015	J	`jnl`	Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nat. 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, Bernd Bukau
2015	J	`jnl`	LigDig: a web server for querying ligand-protein interactions. Bioinform. Jonathan C. Fuller, Michael Martinez, Stefan Henrich, Antonia Stank, Stefan Richter, Rebecca C. Wade
2015	J	`jnl`	SDA 7: A modular and parallel implementation of the simulation of diffusional association software. J. Comput. Chem. Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. Wade
2015	J	`jnl`	webSDA: a web server to simulate macromolecular diffusional association. Nucleic Acids Res. Xiaofeng Yu, Michael Martinez, Annika L. Gable, Jonathan C. Fuller, Neil J. Bruce, Stefan Richter, Rebecca C. Wade
2013	J	`jnl`	Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria. PLoS Comput. Biol. Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer, Rebecca C. Wade
2013	J	`jnl`	TRAPP: A Tool for Analysis of J. Chem. Inf. Model. Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade
2013	J	`jnl`	Targeting protein dynamics in drug design. J. Cheminformatics Rebecca C. Wade
2011	J	`jnl`	Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9. PLoS Comput. Biol. Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom, Rebecca C. Wade
2008	J	`jnl`	SYCAMORE - a systems biology computational analysis and modeling research environment. Bioinform. Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade, Ursula Kummer
2008	J	`jnl`	webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acids Res. Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline, Rebecca C. Wade
2007	J	`jnl`	qPIPSA: Relating enzymatic kinetic parameters and interaction fields. BMC Bioinform. Razif R. Gabdoulline, Matthias Stein, Rebecca C. Wade
2006	J	`jnl`	ProSAT2 - Protein Structure Annotation Server. Nucleic Acids Res. Razif R. Gabdoulline, S. Ulbrich, Stefan Richter, Rebecca C. Wade
2003	J	`jnl`	A New Approach To Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the log J. Chem. Inf. Comput. Sci. Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade, Michael Ramek, Stavroula Piperaki, Anna Tsantili-Kakoulidou, Sanja Tomic
2003	J	`jnl`	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. Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský
2003	J	`jnl`	DSMM: a Database of Simulated Molecular Motions. Nucleic Acids Res. Giacomo Finocchiaro, Ting Wang, René Hoffmann, Aitor González, Rebecca C. Wade
2003	J	`jnl`	MolSurfer: a macromolecular interface navigator. Nucleic Acids Res. Razif R. Gabdoulline, Rebecca C. Wade, Dirk Walther
2003	J	`jnl`	ProSAT: functional annotation of protein 3D structures. Bioinform. Razif R. Gabdoulline, René Hoffmann, Florian Leitner, Rebecca C. Wade
2001	—	`conf`	3D modeling of macromolecular structures and reactions in the context of genomes. German Conference on Bioinformatics Razif R. Gabdoulline, Aitor González, Rebecca C. Wade
1998	J	`jnl`	Classification of auxin plant hormones by interaction property similarity indices. J. Comput. Aided Mol. Des. Sanja Tomic, Razif R. Gabdoulline, Biserka Kojic-Prodic, Rebecca C. Wade
1997	J	`jnl`	Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comput. Chem. Volkhard Helms, Rebecca C. Wade
1990	J	`jnl`	Solvation of the active site of cytochrome P450-cam. J. Comput. Aided Mol. Des. Rebecca C. Wade