Maxim Totrov

Summary

Affiliation: Molsoft LLC
Country: USA

Publications

  1. pmc Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, La Jolla, CA 92037, USA
    BMC Bioinformatics 12:S35. 2011
  2. pmc Estimated Secondary Structure Propensities within V1/V2 Region of HIV gp120 Are an Important Global Antibody Neutralization Sensitivity Determinant
    Maxim Totrov
    Molsoft LLC, San Diego, California, United States of America
    PLoS ONE 9:e94002. 2014
  3. doi request reprint Loop simulations
    Maxim Totrov
    Molsoft L L C, San Diego, CA, USA
    Methods Mol Biol 857:207-29. 2012
  4. pmc Flexible ligand docking to multiple receptor conformations: a practical alternative
    Maxim Totrov
    Molsoft, 3366 N Torrey Pines Court, Suite 300, CA 92037, United States
    Curr Opin Struct Biol 18:178-84. 2008
  5. pmc Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, La Jolla, CA 92037, USA
    Virology 405:513-23. 2010
  6. ncbi request reprint Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, Ste 300, La Jolla CA 92037, USA
    Chem Biol Drug Des 71:15-27. 2008
  7. ncbi request reprint Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, Ste 300, La Jolla, California 92037, USA
    J Comput Chem 25:609-19. 2004
  8. ncbi request reprint Pocketome via comprehensive identification and classification of ligand binding envelopes
    Jianghong An
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Mol Cell Proteomics 4:752-61. 2005
  9. ncbi request reprint Comprehensive identification of "druggable" protein ligand binding sites
    Jianghong An
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Inform 15:31-41. 2004
  10. pmc Docking and scoring with ICM: the benchmarking results and strategies for improvement
    Marco A C Neves
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    J Comput Aided Mol Des 26:675-86. 2012

Research Grants

Detail Information

Publications26

  1. pmc Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, La Jolla, CA 92037, USA
    BMC Bioinformatics 12:S35. 2011
    ..Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB...
  2. pmc Estimated Secondary Structure Propensities within V1/V2 Region of HIV gp120 Are an Important Global Antibody Neutralization Sensitivity Determinant
    Maxim Totrov
    Molsoft LLC, San Diego, California, United States of America
    PLoS ONE 9:e94002. 2014
    ..Recent X-ray structures revealed presence of well-defined tertiary structure within this domain but also demonstrated partial disorder and conformational heterogeneity...
  3. doi request reprint Loop simulations
    Maxim Totrov
    Molsoft L L C, San Diego, CA, USA
    Methods Mol Biol 857:207-29. 2012
    ..Major current challenges are the simulations of loops longer than 12-13 residues, the modeling of multiple interacting flexible loops, and the sensitivity of the loop predictions to the accuracy of the loop environment...
  4. pmc Flexible ligand docking to multiple receptor conformations: a practical alternative
    Maxim Totrov
    Molsoft, 3366 N Torrey Pines Court, Suite 300, CA 92037, United States
    Curr Opin Struct Biol 18:178-84. 2008
    ..In several cases, such an approach has led to experimentally validated predictions...
  5. pmc Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, La Jolla, CA 92037, USA
    Virology 405:513-23. 2010
    ..The short V3-CTB was ineffective. The results suggest that very narrow antigenic profile of an immunogen is associated with poor Ab response. An immunogen with broader antigenic activity elicits robust Ab response...
  6. ncbi request reprint Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, Ste 300, La Jolla CA 92037, USA
    Chem Biol Drug Des 71:15-27. 2008
    ..The new methods are shown to perform competitively in comparison to current state-of-the-art methods...
  7. ncbi request reprint Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking
    Maxim Totrov
    Molsoft LLC, 3366 N Torrey Pines Ct, Ste 300, La Jolla, California 92037, USA
    J Comput Chem 25:609-19. 2004
    ..9. The new GB approximation is also tested in Monte Carlo docking simulations of the fully flexible p53 peptide fragment to MDM2. The best energy solution found in the simulations has RMSD of 2.8 A to the X-ray structure...
  8. ncbi request reprint Pocketome via comprehensive identification and classification of ligand binding envelopes
    Jianghong An
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Mol Cell Proteomics 4:752-61. 2005
    ..The pocketome can be used for rapid evaluation of possible binding partners of a given chemical compound...
  9. ncbi request reprint Comprehensive identification of "druggable" protein ligand binding sites
    Jianghong An
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Inform 15:31-41. 2004
    ..Furthermore, the known and the predicted binding pockets for the proteome of a particular organism can be clustered into a "pocketome", that can be used for rapid evaluation of possible binding partners of a given chemical compound...
  10. pmc Docking and scoring with ICM: the benchmarking results and strategies for improvement
    Marco A C Neves
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    J Comput Aided Mol Des 26:675-86. 2012
    ..2 and ROC((2%)) = 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target...
  11. ncbi request reprint Identification of protein-protein interaction sites from docking energy landscapes
    Juan Fernandez-Recio
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 335:843-65. 2004
    ..This approach can guide the design of mutations on the surfaces of proteins, provide geometrical details of a possible interaction, and help to annotate protein surfaces in structural proteomics...
  12. pmc Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking
    Matthieu Schapira
    Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 100:7354-9. 2003
    ..The extreme structural diversity of the antagonist compounds shows how receptor-based virtual screening can identify diverse chemistries that comply with the structural rules of TR antagonism...
  13. pmc Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking
    Giovanni Bottegoni
    Department of Molecular Biology, The Scripps Research Institute, TPC28, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Med Chem 52:397-406. 2009
    ..3% of the benchmark cases, matching the success rate of the traditional approach but employed on average only one-fourth of the time during the ligand sampling phase...
  14. pmc A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    Giovanni Bottegoni
    Department of Molecular Biology, TPC28, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
    J Comput Aided Mol Des 22:311-25. 2008
    ..Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability...
  15. pmc Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling
    Yelena A Arnautova
    Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA
    Proteins 79:477-98. 2011
    ..We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method...
  16. ncbi request reprint ICM-DISCO docking by global energy optimization with fully flexible side-chains
    Juan Fernandez-Recio
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 52:113-7. 2003
    ..The procedure is global and fully automated. We demonstrate that the algorithm handles the induced changes of surface side-chains but is less successful if the backbone undergoes large-scale rearrangements...
  17. ncbi request reprint Comparative study of several algorithms for flexible ligand docking
    Badry D Bursulaya
    Department of Molecular Biology TPC6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Comput Aided Mol Des 17:755-63. 2003
    ..5% of the top scoring solutions found with ICM and among approximately 9% of the top scoring solutions produced by DOCK and FlexX...
  18. pmc Soft protein-protein docking in internal coordinates
    Juan Fernandez-Recio
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Protein Sci 11:280-91. 2002
    ..The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web...
  19. pmc BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry
    Manuel Rueda
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    BMC Struct Biol 13:32. 2013
    ..Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser...
  20. ncbi request reprint PIER: protein interface recognition for structural proteomics
    Irina Kufareva
    Scripps Research Institute, La Jolla, California 92037, USA
    Proteins 67:400-17. 2007
    ..The accuracy, efficiency, and dependence on structure alone make PIER a suitable tool for automated high-throughput annotation of protein structures emerging from structural proteomics projects...
  21. ncbi request reprint Nuclear hormone receptor targeted virtual screening
    Matthieu Schapira
    Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA
    J Med Chem 46:3045-59. 2003
    ..These data represent a realistic snapshot of the state-of-the-art of NR-targeted VLS and define the recent progress and the remaining limitations of the technology...
  22. ncbi request reprint Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
    VSEVOLOD KATRITCH
    SIGA Technologies, Inc, Corvallis, OR, USA
    J Comput Aided Mol Des 21:549-58. 2007
    ..Thus, fragments predicted to bind in the prime portion of the active site can be combined with fragments on non-prime side to yield compounds with improved activity and specificity...
  23. pmc Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine
    Matthieu Schapira
    Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA
    BMC Struct Biol 2:1. 2002
    ..Ligands that discriminate between the different isotypes of nicotinic acetylcholine receptors (nAChRs) could present improved pharmacology and toxicity profile...
  24. ncbi request reprint A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening
    Michael H Howard
    DuPont Crop Protection, Stine Haskell Research Center, 1094 Elkton Road, Newark, DE 19711, USA
    J Med Chem 47:6669-72. 2004
    ..Data mining and analogue synthesis established a structure--activity relationship for the side chain region that is consistent with the docked structure...
  25. ncbi request reprint Improving CAPRI predictions: optimized desolvation for rigid-body docking
    Juan Fernandez-Recio
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 60:308-13. 2005
    ..In summary, our success rate (89%) shows a consistent improvement over the previous CAPRI rounds, and suggests that a correct desolvation description is key for improved protein-protein docking predictions...
  26. pmc Functional conservation of Rel binding sites in drosophilid genomes
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom
    Genome Res 17:1327-35. 2007
    ..We discuss how two types of conservation may contribute to the stabilization and optimization of a functional gene regulatory code in evolution...

Research Grants4

  1. Rational Development of TCF/Beta-Catenin Antagonists
    Maxim Totrov; Fiscal Year: 2004
    ....
  2. RATIONAL DEVELOPMENT OF THYROID RECEPTOR ANTAGONISTS
    Maxim Totrov; Fiscal Year: 2004
    ..abstract_text> ..
  3. Rational Design of Inhibitors of Yersinia pestis EF-Tu
    Maxim Totrov; Fiscal Year: 2004
    ..abstract_text> ..
  4. Integrated Protein Surface Annotation Suite
    Maxim Totrov; Fiscal Year: 2006
    ..The surface annotation suite will be marketed as a separate module for the ICM molecular modelling package and oriented towards use by biologists and biochemists. [unreadable] [unreadable] [unreadable]..