Jacob D Durrant

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Comparing neural-network scoring functions and the state of the art: applications to common library screening
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
    J Chem Inf Model 53:1726-35. 2013
  2. pmc AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    J Mol Graph Model 44:104-12. 2013
  3. pmc AutoClickChem: click chemistry in silico
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 8:e1002397. 2012
  4. pmc NNScore 2.0: a neural-network receptor-ligand scoring function
    Jacob 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
  5. pmc Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors
    Jacob 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
  6. pmc Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design
    Jacob 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
  7. pmc Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, USA
    BMC Pharmacol 11:9. 2011
  8. pmc HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
    Jacob 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
  9. pmc Molecular dynamics simulations and drug discovery
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    BMC Biol 9:71. 2011
  10. pmc BINANA: a novel algorithm for ligand-binding characterization
    Jacob 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

Detail Information

Publications25

  1. pmc Comparing neural-network scoring functions and the state of the art: applications to common library screening
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
    J Chem Inf Model 53:1726-35. 2013
    ..Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design. ..
  2. pmc AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    J Mol Graph Model 44:104-12. 2013
    ..AutoGrow 3.0 is available free of charge (http://autogrow.ucsd.edu) under the terms of the GNU General Public License and has been tested on Linux and Mac OS X. ..
  3. pmc AutoClickChem: click chemistry in silico
    Jacob 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...
  4. pmc NNScore 2.0: a neural-network receptor-ligand scoring function
    Jacob 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/ ...
  5. pmc Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors
    Jacob 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...
  6. pmc Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design
    Jacob 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...
  7. pmc Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors
    Jacob 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...
  8. pmc HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
    Jacob 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...
  9. pmc Molecular dynamics simulations and drug discovery
    Jacob 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...
  10. pmc BINANA: a novel algorithm for ligand-binding characterization
    Jacob 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...
  11. pmc AutoGrow: a novel algorithm for protein inhibitor design
    Jacob 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...
  12. pmc A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology
    Jacob 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...
  13. pmc Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design
    Jacob 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...
  14. pmc Computational identification of uncharacterized cruzain binding sites
    Jacob 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...
  15. pmc Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness
    Jacob 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...
  16. pmc NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes
    Jacob 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...
  17. pmc Computer-aided drug-discovery techniques that account for receptor flexibility
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    Curr Opin Pharmacol 10:770-4. 2010
    ....
  18. pmc POVME: an algorithm for measuring binding-pocket volumes
    Jacob 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...
  19. pmc CrystalDock: a novel approach to fragment-based drug design
    Jacob 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...
  20. pmc LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders
    Steffen 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...
  21. pmc Novel cruzain inhibitors for the treatment of Chagas' disease
    Kathleen 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...
  22. pmc The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness
    Aaron 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...
  23. pmc Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target
    William 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...
  24. pmc Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1
    Jacob 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...
  25. pmc Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors
    Jacob 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...