Protein binding pocket dynamics A Stank, DB Kokh, JC Fuller, RC Wade Accounts of chemical research 49 (5), 809-815, 2016 | 355 | 2016 |
Modeling and simulation of protein–surface interactions: achievements and challenges M Ozboyaci, DB Kokh, S Corni, RC Wade Quarterly reviews of biophysics 49, e4, 2016 | 230 | 2016 |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding M Amaral, DB Kokh, J Bomke, A Wegener, HP Buchstaller, ... Nature communications 8 (1), 2276, 2017 | 224 | 2017 |
Estimation of drug-target residence times by τ-random acceleration molecular dynamics simulations DB Kokh, M Amaral, J Bomke, U Grädler, D Musil, HP Buchstaller, ... Journal of chemical theory and computation 14 (7), 3859-3869, 2018 | 197 | 2018 |
Kinetics for Drug Discovery: an industry-driven effort to target drug residence time DA Schuetz, WEA de Witte, YC Wong, B Knasmueller, L Richter, DB Kokh, ... Drug discovery today 22 (6), 896-911, 2017 | 196 | 2017 |
Docking of ubiquitin to gold nanoparticles G Brancolini, DB Kokh, L Calzolai, RC Wade, S Corni ACS nano 6 (11), 9863-9878, 2012 | 159 | 2012 |
New approaches for computing ligand–receptor binding kinetics NJ Bruce, GK Ganotra, DB Kokh, SK Sadiq, RC Wade Current opinion in structural biology 49, 1-10, 2018 | 140 | 2018 |
On the ultraviolet photofragmentation of hydrogen iodide AB Alekseyev, HP Liebermann, DB Kokh, RJ Buenker The Journal of Chemical Physics 113 (15), 6174-6185, 2000 | 86 | 2000 |
Protein–surface interactions: challenging experiments and computations O Cohavi, S Corni, F De Rienzo, R Di Felice, KE Gottschalk, M Hoefling, ... Journal of Molecular Recognition: An Interdisciplinary Journal 23 (3), 259-262, 2010 | 79 | 2010 |
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins DB Kokh, S Richter, S Henrich, P Czodrowski, F Rippmann, RC Wade Journal of chemical information and modeling 53 (5), 1235-1252, 2013 | 77 | 2013 |
ProMetCS: An atomistic force field for modeling protein− metal surface interactions in a continuum aqueous solvent DB Kokh, S Corni, PJ Winn, M Hoefling, KE Gottschalk, RC Wade Journal of Chemical Theory and Computation 6 (5), 1753-1768, 2010 | 73 | 2010 |
SDA 7: A modular and parallel implementation of the simulation of diffusional association software M Martinez, NJ Bruce, J Romanowska, DB Kokh, M Ozboyaci, X Yu, ... Journal of computational chemistry 36 (21), 1631-1645, 2015 | 68 | 2015 |
Receptor flexibility in small‐molecule docking calculations DB Kokh, RC Wade, W Wenzel Wiley Interdisciplinary Reviews: Computational Molecular Science 1 (2), 298-314, 2011 | 67 | 2011 |
Recent progress in molecular simulation methods for drug binding kinetics A Nunes-Alves, DB Kokh, RC Wade Current Opinion in Structural Biology 64, 126-133, 2020 | 65 | 2020 |
Flexible side chain models improve enrichment rates in in silico screening DB Kokh, W Wenzel Journal of medicinal chemistry 51 (19), 5919-5931, 2008 | 65 | 2008 |
A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand … DB Kokh, B Doser, S Richter, F Ormersbach, X Cheng, RC Wade The Journal of chemical physics 153 (12), 2020 | 61 | 2020 |
A comparative study of the electron distribution function in the positive columns in and/He dc glow discharges by optical spectroscopy and probes NK Bibinov, DB Kokh, NB Kolokolov, VA Kostenko, D Meyer, ... Plasma Sources Science and Technology 7 (3), 298, 1998 | 61 | 1998 |
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets A Stank, DB Kokh, M Horn, E Sizikova, R Neil, J Panecka, S Richter, ... Nucleic acids research 45 (W1), W325-W330, 2017 | 55 | 2017 |
The 'approach-induced' I2(E0+g ↔ I2(X) D0+u) transition ME Akopyan, NK Bibinov, DB Kokh, AM Pravilov, MB Stepanov, ... Chem. Phys. 242 (2), 263-272, 1999 | 50 | 1999 |
Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2 BT Berger, M Amaral, DB Kokh, A Nunes-Alves, D Musil, T Heinrich, ... Cell Chemical Biology 28 (5), 686-698. e7, 2021 | 46 | 2021 |