Research Topics
| Jacob D DurrantSummaryAffiliation: University of California Country: USA Publications
| Collaborators
|
Detail Information
Publications
AutoClickChem: click chemistry in silicoJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
PLoS Comput Biol 8:e1002397. 2012..Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu...- NNScore 2.0: a neural-network receptor-ligand scoring functionJacob D Durrant
Department of Chemistry and Biochemistry and Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA
J Chem Inf Model 51:2897-903. 2011..0 provides a single estimate of the pK(d). To facilitate use, NNScore 2.0 has been implemented as an open-source python script. A copy can be obtained from http://www.nbcr.net/software/nnscore/ ... - AutoGrow: a novel algorithm for protein inhibitor designJacob D Durrant
Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093 0365, USA
Chem Biol Drug Des 73:168-78. 2009..To validate AutoGrow, we recreate three crystallographically resolved ligands from their constituent fragments... - Molecular dynamics simulations and drug discoveryJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
BMC Biol 9:71. 2011..With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role... - HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysisJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, United States
J Mol Graph Model 31:5-9. 2011..Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza... - Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitorsJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, USA
BMC Pharmacol 11:9. 2011..brucei drug target RNA editing ligase 1, in order to improve its predicted binding affinity... - Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug designJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, CA 92093, USA
Chem Biol Drug Des 78:323-32. 2011..These results are of interest because farnesyl diphosphate synthase inhibitors are being pursued as both anti-infective and anticancer agents, and undecaprenyl diphosphate synthase inhibitors are antibacterial drug leads... - Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitorsJacob D Durrant
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 0365, USA
Chem Biol Drug Des 78:191-8. 2011..Consequently, when attempting to predict ligand affinity and selectivity using an ensemble of protein structures, it may be wise to disregard protein conformations that cannot accommodate the ligand... - BINANA: a novel algorithm for ligand-binding characterizationJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, United States
J Mol Graph Model 29:888-93. 2011..We are hopeful that BINANA will be useful to computational chemists and structural biologists who wish to automatically characterize many ligand-receptor complexes for key binding characteristics... - POVME: an algorithm for measuring binding-pocket volumesJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, USA
J Mol Graph Model 29:773-6. 2011..Despite the structural similarity of these proteins, differences in binding-pocket dynamics are easily identified... - Computer-aided drug-discovery techniques that account for receptor flexibilityJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
Curr Opin Pharmacol 10:770-4. 2010.... - NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexesJacob D Durrant
Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093, USA
J Chem Inf Model 50:1865-71. 2010..The scoring function presented here, used either on its own or in conjunction with other more traditional functions, could prove useful in future drug-discovery efforts... - Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sicknessJacob D Durrant
Biomedical Sciences Program, University of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093 0365, USA
J Med Chem 53:5025-32. 2010..Thirteen of these inhibitors belong to a distinct series with a conserved binding motif that may prove useful in future drug design and optimization... - Computational identification of uncharacterized cruzain binding sitesJacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
PLoS Negl Trop Dis 4:e676. 2010..The two sites identified may serve as targets for future pharmacological intervention... - A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homologyJacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 6:e1000648. 2010..As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology... - Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug designJacob D Durrant
Biomedical Sciences Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, United States
Comput Biol Chem 34:97-105. 2010..Several potential inhibitors are identified that are predicted to bind to neuraminidase better than currently approved drugs... - CrystalDock: a novel approach to fragment-based drug designJacob D Durrant
Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, United States
J Chem Inf Model 51:2573-80. 2011..In both cases, CrystalDock suggests modifications to known inhibitors that may improve binding affinity... - The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sicknessAaron J Friedman
Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093 0365, USA
Chem Biol Drug Des 80:173-81. 2012..This dependence provides important insights into TbGalE function and may help guide future computer-aided drug discovery efforts targeting this protein... - Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial targetWilliam Sinko
Department of Chemistry and Biochemistry, and NSF Center for Theoretical Biological Physics, University of California San Diego, La Jolla, USA
Chem Biol Drug Des 77:412-20. 2011..We believe that this is the first time that a rare 'expanded pocket' state, key to drug design and verified by crystallography, has been extracted from a molecular dynamics simulation... - Novel cruzain inhibitors for the treatment of Chagas' diseaseKathleen E Rogers
Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, 92093, USA
Chem Biol Drug Des 80:398-405. 2012..Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas' disease... - Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1Jacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
PLoS Negl Trop Dis 4:e803. 2010..RNA Editing Ligase 1 (REL1), a protein unique to trypanosomes and other kinetoplastids, was identified recently as a potential drug target... - Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitorsJacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California 92093 0365, USA
J Mol Recognit 23:173-82. 2010..Our strategy identifies molecular fragments predicted to target multiple MMP-2 binding pockets... - LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known bindersSteffen Lindert
Department of Pharmacology, University of California San Diego, La Jolla, 92093, USA
Chem Biol Drug Des 80:358-65. 2012..We hope that LigMerge will be a helpful tool for the drug design community...