Research Topics
| Maxim TotrovSummaryAffiliation: Molsoft LLC Country: USA Publications
Research Grants
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Detail Information
Publications
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sitesMaxim 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...
Loop simulationsMaxim 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...
Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSARMaxim 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...- Flexible ligand docking to multiple receptor conformations: a practical alternativeMaxim 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... - Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide dockingMaxim 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... - Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffoldMaxim 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... - Pocketome via comprehensive identification and classification of ligand binding envelopesJianghong 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... - Comprehensive identification of "druggable" protein ligand binding sitesJianghong An
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Genome Inform 15:31-41. 2004.... - Docking and scoring with ICM: the benchmarking results and strategies for improvementMarco 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... - Identification of protein-protein interaction sites from docking energy landscapesJuan 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... - ICM-DISCO docking by global energy optimization with fully flexible side-chainsJuan 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... - Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand dockingGiovanni 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... - Discovery of diverse thyroid hormone receptor antagonists by high-throughput dockingMatthieu 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... - 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... - Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modelingYelena 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... - Soft protein-protein docking in internal coordinatesJuan 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... - Comparative study of several algorithms for flexible ligand dockingBadry 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... - Nuclear hormone receptor targeted virtual screeningMatthieu 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... - PIER: protein interface recognition for structural proteomicsIrina 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... - Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approachesVSEVOLOD 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... - Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotineMatthieu 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... - Functional conservation of Rel binding sites in drosophilid genomesRichard 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... - Improving CAPRI predictions: optimized desolvation for rigid-body dockingJuan 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... - A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screeningMichael 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...
Research Grants
- Rational Development of TCF/Beta-Catenin AntagonistsMaxim Totrov; Fiscal Year: 2004....
- RATIONAL DEVELOPMENT OF THYROID RECEPTOR ANTAGONISTSMaxim Totrov; Fiscal Year: 2004..abstract_text> ..
- Rational Design of Inhibitors of Yersinia pestis EF-TuMaxim Totrov; Fiscal Year: 2004..abstract_text> ..
- Integrated Protein Surface Annotation SuiteMaxim 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. ..