| Year |
Citation |
Score |
| 2023 |
Ahmed M, Maldonado AM, Durrant JD. From byte to bench to bedside: molecular dynamics simulations and drug discovery. Bmc Biology. 21: 299. PMID 38155355 DOI: 10.1186/s12915-023-01791-z |
0.314 |
|
| 2023 |
Ahmed M, Maldonado AM, Durrant JD. From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery. Arxiv. PMID 38076508 |
0.314 |
|
| 2023 |
Bhatt R, Koes DR, Durrant JD. CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Biorxiv : the Preprint Server For Biology. PMID 37904961 DOI: 10.1101/2023.10.18.562959 |
0.304 |
|
| 2023 |
Hellemann E, Durrant JD. Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling. Journal of Chemical Theory and Computation. 19: 5677-5689. PMID 37585617 DOI: 10.1021/acs.jctc.3c00478 |
0.346 |
|
| 2023 |
Hellemann E, Durrant JD. Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling. Biorxiv : the Preprint Server For Biology. PMID 37251500 DOI: 10.1101/2023.05.03.539330 |
0.346 |
|
| 2023 |
van Wieren A, Durrant JD, Majumdar S. Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics. Drug Development Research. PMID 37129190 DOI: 10.1002/ddr.22068 |
0.318 |
|
| 2021 |
Green H, Koes DR, Durrant JD. DeepFrag: a deep convolutional neural network for fragment-based lead optimization. Chemical Science. 12: 8036-8047. PMID 34194693 DOI: 10.1039/d1sc00163a |
0.323 |
|
| 2021 |
Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. Dna Repair. 103: 103125. PMID 33940558 DOI: 10.1016/j.dnarep.2021.103125 |
0.737 |
|
| 2020 |
Spiegel JO, Durrant JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. Journal of Cheminformatics. 12: 25. PMID 33431021 DOI: 10.1186/s13321-020-00429-4 |
0.785 |
|
| 2020 |
Kochnev Y, Hellemann E, Cassidy KC, Durrant JD. Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser. Bioinformatics (Oxford, England). PMID 32559277 DOI: 10.1093/Bioinformatics/Btaa579 |
0.395 |
|
| 2020 |
Cassidy KC, Šefčík J, Raghav Y, Chang A, Durrant JD. ProteinVR: Web-based molecular visualization in virtual reality. Plos Computational Biology. 16: e1007747. PMID 32231351 DOI: 10.1371/Journal.Pcbi.1007747 |
0.36 |
|
| 2020 |
Durrant JD, Kochanek SE, Casalino L, Ieong PU, Dommer AC, Amaro RE. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. Acs Central Science. 6: 189-196. PMID 32123736 DOI: 10.1021/Acscentsci.9B01071 |
0.368 |
|
| 2020 |
Spiegel JO, Durrant JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization Journal of Cheminformatics. 12. DOI: 10.1186/S13321-020-00429-4 |
0.78 |
|
| 2020 |
Cassidy KC, Kaminsky JC, Berman AJ, Durrant JD. Secondary-Structure Changes Impact LARP1/mRNA Binding: Simulations and Experiments Suggest New Avenues for Anti-Cancer Drug Discovery Biophysical Journal. 118: 297a. DOI: 10.1016/J.Bpj.2019.11.1685 |
0.376 |
|
| 2019 |
Cassidy KC, Lahr RM, Kaminsky JC, Mack S, Fonseca BD, Das SR, Berman AJ, Durrant JD. Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Structure (London, England : 1993). PMID 31676287 DOI: 10.1016/J.Str.2019.10.006 |
0.373 |
|
| 2019 |
Plakke MS, Walker JL, Lombardo JB, Goetz BJ, Pacella GN, Durrant JD, Clark NL, Morehouse NI. Characterization of Female Reproductive Proteases in a Butterfly from Functional and Evolutionary Perspectives. Physiological and Biochemical Zoology : Pbz. 92: 579-590. PMID 31584859 DOI: 10.1086/705722 |
0.331 |
|
| 2019 |
Pacheco S, Kaminsky J, Kochnev I, Durrant JD. PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. Journal of Chemical Information and Modeling. PMID 31580061 DOI: 10.1021/Acs.Jcim.9B00703 |
0.31 |
|
| 2019 |
Ropp PJ, Spiegel JO, Walker JL, Green H, Morales GA, Milliken KA, Ringe JJ, Durrant JD. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. Journal of Cheminformatics. 11: 34. PMID 31127411 DOI: 10.1186/S13321-019-0358-3 |
0.749 |
|
| 2019 |
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD. Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. Journal of Cheminformatics. 11: 14. PMID 30767086 DOI: 10.1186/S13321-019-0336-9 |
0.426 |
|
| 2019 |
Cassidy KC, Lahr RM, Kaminsky JC, Berman AJ, Durrant JD. Capturing the Mechanism Underlying Top-Binding to the LARP1 DM15 Region Biophysical Journal. 116: 434a. DOI: 10.1016/J.Bpj.2018.11.2337 |
0.301 |
|
| 2018 |
Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. Acs Central Science. 4: 1570-1577. PMID 30555910 DOI: 10.1021/Acscentsci.8B00666 |
0.356 |
|
| 2018 |
Durrant JD. BlendMol: Advanced Macromolecular Visualization in Blender. Bioinformatics (Oxford, England). PMID 30481283 DOI: 10.1093/Bioinformatics/Bty968 |
0.305 |
|
| 2018 |
Ottilie S, Goldgof GM, Cheung AL, Walker JL, Vigil E, Allen KE, Antonova-Koch Y, Slayman CW, Suzuki Y, Durrant JD. Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. Journal of Cheminformatics. 10: 6. PMID 29464421 DOI: 10.1186/S13321-018-0261-3 |
0.394 |
|
| 2017 |
Rajendiran N, Durrant JD. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques. Journal of Computational Chemistry. PMID 29280166 DOI: 10.1002/Jcc.25155 |
0.327 |
|
| 2017 |
Ropp P, Friedman A, Durrant JD. Scoria: a Python module for manipulating 3D molecular data. Journal of Cheminformatics. 9: 52. PMID 29086076 DOI: 10.1186/S13321-017-0237-8 |
0.357 |
|
| 2017 |
Abraham MM, Denton RE, Harper RW, Scott WL, O'Donnell MJ, Durrant JD. Documenting and Harnessing the Biological Potential of Molecules in Distributed Drug Discovery (D3) Virtual Catalogs. Chemical Biology & Drug Design. PMID 28453915 DOI: 10.1111/Cbdd.13012 |
0.433 |
|
| 2016 |
Ottilie S, Goldgof GM, Calvet CM, Jennings GK, LaMonte G, Schenken J, Vigil E, Kumar P, McCall LI, Lopes ES, Gunawan F, Yang J, Suzuki Y, Siqueira-Neto JL, McKerrow JH, ... ... Durrant JD, et al. Rapid Chagas disease drug target discovery using directed evolution in drug-sensitive yeast. Acs Chemical Biology. PMID 27977118 DOI: 10.1021/Acschembio.6B01037 |
0.495 |
|
| 2016 |
Goldgof GM, Durrant JD, Ottilie S, Vigil E, Allen KE, Gunawan F, Kostylev M, Henderson KA, Yang J, Schenken J, LaMonte GM, Manary MJ, Murao A, Nachon M, Stanhope R, et al. Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Scientific Reports. 6: 27806. PMID 27291296 DOI: 10.1038/Srep27806 |
0.305 |
|
| 2016 |
Durrant JD, Bush RM, Amaro RE. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants. The Journal of Physical Chemistry. B. PMID 27141956 DOI: 10.1021/Acs.Jpcb.6B02655 |
0.376 |
|
| 2016 |
Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chemical Reviews. PMID 27074285 DOI: 10.1021/Acs.Chemrev.5B00631 |
0.63 |
|
| 2015 |
Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro RE. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. Journal of Chemical Information and Modeling. 55: 1953-61. PMID 26286148 DOI: 10.1021/Acs.Jcim.5B00241 |
0.457 |
|
| 2015 |
Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro RE, Wahab HA. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. Journal of Chemical Information and Modeling. 55: 308-16. PMID 25555059 DOI: 10.1021/Ci500405G |
0.363 |
|
| 2015 |
Durrant JD, Amaro RE. Machine-learning techniques applied to antibacterial drug discovery. Chemical Biology & Drug Design. 85: 14-21. PMID 25521642 DOI: 10.1111/Cbdd.12423 |
0.347 |
|
| 2015 |
Scott WL, Denton RE, Marrs KA, Durrant JD, Samaritoni JG, Abraham MM, Brown SP, Carnahan JM, Fischer LG, Glos CE, Sempsrott PJ, O'Donnell MJ. Distributed drug discovery: Advancing chemical education through contextualized combinatorial solid-phase organic laboratories Journal of Chemical Education. 92: 819-826. DOI: 10.1021/Ed500135N |
0.379 |
|
| 2014 |
Durrant JD, Votapka L, Sørensen J, Amaro RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. Journal of Chemical Theory and Computation. 10: 5047-5056. PMID 25400521 DOI: 10.1021/Ct500381C |
0.451 |
|
| 2014 |
Tallorin L, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorganic & Medicinal Chemistry. 22: 6053-61. PMID 25284249 DOI: 10.1016/J.Bmc.2014.09.002 |
0.517 |
|
| 2014 |
Durrant JD, Amaro RE. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. Bmc Bioinformatics. 15: 159. PMID 24886360 DOI: 10.1186/1471-2105-15-159 |
0.369 |
|
| 2014 |
Van Wart AT, Durrant J, Votapka L, Amaro RE. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. Journal of Chemical Theory and Computation. 10: 511-517. PMID 24803851 DOI: 10.1021/Ct4008603 |
0.403 |
|
| 2014 |
Feher VA, Durrant JD, Van Wart AT, Amaro RE. Computational approaches to mapping allosteric pathways. Current Opinion in Structural Biology. 25: 98-103. PMID 24667124 DOI: 10.1016/J.Sbi.2014.02.004 |
0.37 |
|
| 2013 |
Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. Journal of Molecular Graphics & Modelling. 44: 104-12. PMID 23792207 DOI: 10.1016/J.Jmgm.2013.05.006 |
0.609 |
|
| 2013 |
Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. Journal of Chemical Information and Modeling. 53: 1726-35. PMID 23734946 DOI: 10.1021/Ci400042Y |
0.529 |
|
| 2012 |
Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. Novel cruzain inhibitors for the treatment of Chagas' disease. Chemical Biology & Drug Design. 80: 398-405. PMID 22613098 DOI: 10.1111/J.1747-0285.2012.01416.X |
0.527 |
|
| 2012 |
Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chemical Biology & Drug Design. 80: 358-65. PMID 22594624 DOI: 10.1111/J.1747-0285.2012.01414.X |
0.592 |
|
| 2012 |
Friedman AJ, Durrant JD, Pierce LC, McCorvie TJ, Timson DJ, McCammon JA. The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. Chemical Biology & Drug Design. 80: 173-81. PMID 22487100 DOI: 10.1111/J.1747-0285.2012.01392.X |
0.537 |
|
| 2012 |
Durrant JD, McCammon JA. AutoClickChem: click chemistry in silico. Plos Computational Biology. 8: e1002397. PMID 22438795 DOI: 10.1371/Journal.Pcbi.1002397 |
0.548 |
|
| 2011 |
Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. Bmc Biology. 9: 71. PMID 22035460 DOI: 10.1186/1741-7007-9-71 |
0.597 |
|
| 2011 |
Durrant JD, McCammon JA. NNScore 2.0: a neural-network receptor-ligand scoring function. Journal of Chemical Information and Modeling. 51: 2897-903. PMID 22017367 DOI: 10.1021/Ci2003889 |
0.488 |
|
| 2011 |
Durrant JD, Friedman AJ, McCammon JA. CrystalDock: a novel approach to fragment-based drug design. Journal of Chemical Information and Modeling. 51: 2573-80. PMID 21910501 DOI: 10.1021/Ci200357Y |
0.595 |
|
| 2011 |
Durrant JD, McCammon JA. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. Journal of Molecular Graphics & Modelling. 31: 5-9. PMID 21880522 DOI: 10.1016/J.Jmgm.2011.07.008 |
0.458 |
|
| 2011 |
Durrant JD, McCammon JA. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. Bmc Pharmacology. 11: 9. PMID 21878090 DOI: 10.1186/1471-2210-11-9 |
0.551 |
|
| 2011 |
Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chemical Biology & Drug Design. 78: 323-32. PMID 21696546 DOI: 10.1111/J.1747-0285.2011.01164.X |
0.537 |
|
| 2011 |
Durrant JD, de Oliveira CA, McCammon JA. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chemical Biology & Drug Design. 78: 191-8. PMID 21609408 DOI: 10.1111/J.1747-0285.2011.01148.X |
0.507 |
|
| 2011 |
Durrant JD, McCammon JA. BINANA: a novel algorithm for ligand-binding characterization. Journal of Molecular Graphics & Modelling. 29: 888-93. PMID 21310640 DOI: 10.1016/J.Jmgm.2011.01.004 |
0.538 |
|
| 2011 |
Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chemical Biology & Drug Design. 77: 412-20. PMID 21294851 DOI: 10.1111/J.1747-0285.2011.01101.X |
0.755 |
|
| 2011 |
Durrant JD, de Oliveira CA, McCammon JA. POVME: an algorithm for measuring binding-pocket volumes. Journal of Molecular Graphics & Modelling. 29: 773-6. PMID 21147010 DOI: 10.1016/J.Jmgm.2010.10.007 |
0.551 |
|
| 2010 |
Durrant JD, McCammon JA. Computer-aided drug-discovery techniques that account for receptor flexibility. Current Opinion in Pharmacology. 10: 770-4. PMID 20888294 DOI: 10.1016/J.Coph.2010.09.001 |
0.539 |
|
| 2010 |
Durrant JD, McCammon JA. NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. Journal of Chemical Information and Modeling. 50: 1865-71. PMID 20845954 DOI: 10.1021/Ci100244V |
0.531 |
|
| 2010 |
Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE. Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. Plos Neglected Tropical Diseases. 4: e803. PMID 20808768 DOI: 10.1371/Journal.Pntd.0000803 |
0.468 |
|
| 2010 |
Durrant JD, Urbaniak MD, Ferguson MA, McCammon JA. Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. Journal of Medicinal Chemistry. 53: 5025-32. PMID 20527952 DOI: 10.1021/Jm100456A |
0.555 |
|
| 2010 |
Durrant JD, Keränen H, Wilson BA, McCammon JA. Computational identification of uncharacterized cruzain binding sites. Plos Neglected Tropical Diseases. 4: e676. PMID 20485483 DOI: 10.1371/Journal.Pntd.0000676 |
0.519 |
|
| 2010 |
Durrant JD, McCammon JA. Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Computational Biology and Chemistry. 34: 97-105. PMID 20427241 DOI: 10.1016/J.Compbiolchem.2010.03.005 |
0.558 |
|
| 2010 |
Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. Plos Computational Biology. 6: e1000648. PMID 20098496 DOI: 10.1371/Journal.Pcbi.1000648 |
0.563 |
|
| 2010 |
Durrant JD, de Oliveira CA, McCammon JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. Journal of Molecular Recognition : Jmr. 23: 173-82. PMID 19882751 DOI: 10.1002/Jmr.989 |
0.503 |
|
| 2009 |
Durrant JD, Amaro RE, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chemical Biology & Drug Design. 73: 168-78. PMID 19207419 DOI: 10.1111/J.1747-0285.2008.00761.X |
0.555 |
|
| 2009 |
Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 48: 709-19. PMID 19133737 DOI: 10.1021/Bi8018114 |
0.415 |
|
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