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Daria Kokh - Publications

Affiliations: 
Heidelberg Institute for Theoretical Studies 
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, ... ... Kokh DB, et al. A community effort in SARS-CoV-2 drug discovery. Molecular Informatics. PMID 37833243 DOI: 10.1002/minf.202300262  0.661
2023 Viviani LG, Kokh DB, Wade RC, T-do Amaral A. Molecular Dynamics Simulations of the Human Ecto-5'-Nucleotidase (h-ecto-5'-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. Journal of Chemical Information and Modeling. 63: 4691-4707. PMID 37532679 DOI: 10.1021/acs.jcim.3c01068  0.542
2021 Kokh DB, Wade RC. G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations. Journal of Chemical Theory and Computation. PMID 34495672 DOI: 10.1021/acs.jctc.1c00641  0.591
2021 Bianciotto M, Gkeka P, Kokh DB, Wade RC, Minoux H. Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 34494849 DOI: 10.1021/acs.jctc.1c00453  0.572
2021 Nunes-Alves A, Kokh DB, Wade RC. Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations. Current Research in Structural Biology. 3: 106-111. PMID 34235490 DOI: 10.1016/j.crstbi.2021.04.001  0.579
2021 Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, ... ... Kokh DB, et al. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics. Acs Pharmacology & Translational Science. 4: 1079-1095. PMID 34136757 DOI: 10.1021/acsptsci.0c00215  0.596
2021 Reinhardt M, Bruce NJ, Kokh DB, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics. Journal of Chemical Theory and Computation. PMID 33784462 DOI: 10.1021/acs.jctc.0c01312  0.723
2021 Berger BT, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schröder M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, Müller S, Frech M, Wade RC, et al. Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Cell Chemical Biology. PMID 33497606 DOI: 10.1016/j.chembiol.2021.01.003  0.529
2020 Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC. A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories. The Journal of Chemical Physics. 153: 125102. PMID 33003755 DOI: 10.1063/5.0019088  0.575
2020 Nunes-Alves A, Kokh DB, Wade RC. Recent progress in molecular simulation methods for drug binding kinetics. Current Opinion in Structural Biology. 64: 126-133. PMID 32771530 DOI: 10.1016/J.Sbi.2020.06.022  0.58
2020 Yuan JH, Han SB, Richter S, Wade RC, Kokh DB. Druggability Assessment in TRAPP using Machine Learning Approaches. Journal of Chemical Information and Modeling. PMID 32105476 DOI: 10.1021/Acs.Jcim.9B01185  0.603
2019 Kokh DB, Kaufmann T, Kister B, Wade RC. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times. Frontiers in Molecular Biosciences. 6: 36. PMID 31179286 DOI: 10.3389/Fmolb.2019.00036  0.592
2018 Kokh DB, Amaral M, Bomke J, Grädler U, Musil D, Buchstaller HP, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 29768913 DOI: 10.1021/Acs.Jctc.8B00230  0.548
2017 Amaral M, Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P, Sirrenberg C, Wade RC, Frech M. Protein conformational flexibility modulates kinetics and thermodynamics of drug binding. Nature Communications. 8: 2276. PMID 29273709 DOI: 10.1038/S41467-017-02258-W  0.606
2017 Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. Current Opinion in Structural Biology. 49: 1-10. PMID 29132080 DOI: 10.1016/J.Sbi.2017.10.001  0.753
2017 Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC. TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Research. PMID 28431137 DOI: 10.1093/Nar/Gkx277  0.576
2017 Schuetz DA, de Witte WEA, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, et al. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time. Drug Discovery Today. PMID 28412474 DOI: 10.1016/J.Drudis.2017.02.002  0.532
2016 Kokh DB, Czodrowski P, Rippmann F, Wade RC. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets. Journal of Chemical Theory and Computation. PMID 27399277 DOI: 10.1021/Acs.Jctc.6B00101  0.597
2016 Stank A, Kokh DB, Fuller JC, Wade RC. Protein Binding Pocket Dynamics. Accounts of Chemical Research. 49: 809-15. PMID 27110726 DOI: 10.1021/Acs.Accounts.5B00516  0.61
2016 Ozboyaci M, Kokh DB, Corni S, Wade RC. Modeling and simulation of protein-surface interactions: achievements and challenges. Quarterly Reviews of Biophysics. 49: e4. PMID 26821792 DOI: 10.1017/S0033583515000256  0.794
2016 Ozboyaci M, Kokh DB, Wade RC. Three steps to gold: Mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations Physical Chemistry Chemical Physics. 18: 10191-10200. DOI: 10.1039/c6cp00201c  0.785
2016 Ozboyaci M, Kokh DB, Corni S, Wade RC. Modeling and simulation of protein-surface interactions: Achievements and challenges Quarterly Reviews of Biophysics. 49. DOI: 10.1017/S0033583515000256  0.771
2015 Romanowska J, Kokh DB, Wade RC. When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces. Nano Letters. 15: 7508-13. PMID 26491986 DOI: 10.1021/Acs.Nanolett.5B03168  0.762
2015 Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC. SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of Computational Chemistry. PMID 26123630 DOI: 10.1002/Jcc.23971  0.69
2015 Romanowska J, Kokh DB, Fuller JC, Wade RC. Computational Approaches for Studying Drug Binding Kinetics Thermodynamics and Kinetics of Drug Binding. 211-235. DOI: 10.1002/9783527673025.ch11  0.32
2013 Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC. TRAPP: a tool for analysis of transient binding pockets in proteins. Journal of Chemical Information and Modeling. 53: 1235-52. PMID 23621586 DOI: 10.1021/Ci4000294  0.583
2012 Brancolini G, Kokh DB, Calzolai L, Wade RC, Corni S. Docking of ubiquitin to gold nanoparticles. Acs Nano. 6: 9863-78. PMID 23033917 DOI: 10.1021/Nn303444B  0.498
2011 Mereghetti P, Kokh D, McCammon JA, Wade RC. Diffusion and association processes in biological systems: theory, computation and experiment. Bmc Biophysics. 4: 2. PMID 21595997 DOI: 10.1186/2046-1682-4-2  0.742
2011 Cohavi O, Reichmann D, Abramovich R, Tesler AB, Bellapadrona G, Kokh DB, Wade RC, Vaskevich A, Rubinstein I, Schreiber G. A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 1327-36. PMID 21243701 DOI: 10.1002/Chem.201001781  0.582
2011 Kokh DB, Wade RC, Wenzel W. Receptor flexibility in small‐molecule docking calculations Wires Computational Molecular Science. 1: 298-314. DOI: 10.1002/Wcms.29  0.57
2010 Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent. Journal of Chemical Theory and Computation. 6: 1753-68. PMID 26615704 DOI: 10.1021/Ct100086J  0.598
2010 Cohavi O, Corni S, De Rienzo F, Di Felice R, Gottschalk KE, Hoefling M, Kokh D, Molinari E, Schreiber G, Vaskevich A, Wade RC. Protein-surface interactions: challenging experiments and computations. Journal of Molecular Recognition : Jmr. 23: 259-62. PMID 19950121 DOI: 10.1002/Jmr.993  0.621
2010 Pérez-Sánchez H, Fischer B, Kokh D, Merlitz H, Wenzel W. High throughput in-silico screening against flexible protein receptors Journal of Cheminformatics. 2. DOI: 10.1186/1758-2946-2-S1-P23  0.338
2010 Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An atomistic force field for modeling protein-metal surface interactions in a continuum aqueous solvent Journal of Chemical Theory and Computation. 6: 1753-1768. DOI: 10.1021/ct100086j  0.51
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