Jacob Devin Durrant - Publications

2010 Biomedical Sciences University of California, San Diego, La Jolla, CA 

43 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
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
2014 Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. Plos Computational Biology. 10: e1003720. PMID 25032790 DOI: 10.1371/journal.pcbi.1003720  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
2012 Durrant JD, McCammon JA. AutoClickChem: click chemistry in silico. Plos Computational Biology. 8: e1002397. PMID 22438795 DOI: 10.1371/journal.pcbi.1002397  0.4
2011 Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. Bmc Biology. 9: 71. PMID 22035460 DOI: 10.1186/1741-7007-9-71  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
2006 Durrant JD, Caywood D, Busath DD. Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels. Biophysical Journal. 91: 3230-41. PMID 16861266 DOI: 10.1529/biophysj.105.078782  0.4
2006 Durrant JD, Gardunia BW, Livingstone KD, Stevens MR, Jellen EN. An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap. The Journal of Heredity. 97: 62-6. PMID 16394257 DOI: 10.1093/jhered/esj002  0.4
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