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Forti, F., Cavasotto, C.N., Orozco, M., Barril, X. and Luque, F.J.
A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules.
J. Chem. Theory Comput. 8:1808–1819 (2012).
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Dasgupta, I., Tanifum, E.A., Srivastava, M., Phatak, S.S, Cavasotto, C.N., Analoui, M., and Annapragada, A.
Non inflammatory boronate based glucose-responsive insulin delivery systems.
PLoS ONE 7:e29585 (2012).
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Cavasotto, C.N.
Binding free energy calculation and scoring in small-molecule docking.
In Physico-Chemical and Computational Appraoches to Drug Discovery, Royal Society of Chemistry, Eds. F. Javier Luque and Xavier Barril, in press.
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Gatica, E.A. and Cavasotto, C.N.*
Ligand and decoy sets for docking to G Protein-Coupled Receptors.
J. Chem. Inf. Model. 52:1–6 (2012), http://pubs.acs.org/doi/abs/10.1021/ci200412p.
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Cavasotto, C.N.
Normal-mode-based approaches in receptor ensemble docking.
Methods Mol. Biol. 819:157-168 (2012).
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Echenique P., Cavasotto, C.N., García-Risueño, P.
The canonical equilibrium of constrained molecular models.
Eur. Phys. J. ST, 200:5-54, (2011)
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Anisimov, V.M., Ziemys, A., Kizhake, S., Yuan, Z., Natarajan, A., Cavasotto, C.N.*
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1.
J. Comput-aided Mol. Des. 25:1071-1084 (2011).
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Echenique P., Cavasotto, C.N., De Marco, M., García-Risueño, P., and Alonso, J. L.
Avoiding pitfalls in molecular simulation with flexible constraints.
PLoS ONE, 6:e24563 (2011).
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Anisimov, V.M. and Cavasotto, C.N.
Hydration free energies using semiempirical quantum mechanical Hamiltonians and a continuum solvent model with multiple atomic-type parameters.
J. Phys. Chem. B 115:7896-7905 (2011).
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Anisimov, V.M. and Cavasotto, C.N.
Quantum Mechanical Binding Free-energy Calculation for Phosphopeptide Inhibitors of the Lck SH2 Domain.
J. Comput. Chem. 32:2254-2263 (2011).
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Bocanegra, R., Nevot, M., Domenech, R., López, I., Abián, O., Rodríguez-Huete, A., Cavasotto, C.N., Velázquez-Campoy, A., Gómez, J., Martínez, M.A., Neira, J.L. and Mateu, M.G.
Cocktails of designed interfacial peptides abolish in vitro the assembly of the HIV-1 capsid and inhibit virus infection of cultured cells.
PLoS ONE 6:e23877 (2011).
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Cavasotto, C.N.
Homology models in docking and high-throughput docking.
Curr. Top. Med. Chem. 11:1528-1534 (2011).
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Vilar, S., Ferino, G., Phatak, S.S., Berk, B., Cavasotto, C.N. and Costanzi, S.
Docking-based virtual screening for GPCRs ligands: not only crystal structures but also in silico models.
J. Mol. Graph. Model. 29:614-623 (2011).
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Cavasotto, C.N. and Phatak S.S.
Docking Methods for Structure-based Library Design.
Methods Mol. Biol. 685:155-174 (2011).
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Cavasotto, C.N.
Handling protein flexibility in docking and high-throughput docking: From algorithms to applications.
In Virtual Screening. Principles, Challenges and Practical Guidelines. WILEY-VCH Verlag. Ed. Christoph Sotriffer: 2011; Vol. 48, pp 245-262.
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Phatak, S.S., Gatica, E.A. and Cavasotto, C.N.
Ligand-steered modeling and docking: A benchmarking study in Class A G-Protein Coupled Receptors.
J. Chem. Inf. Model. 50:2119-2128 (2010).
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Anisimov, V.M. and Cavasotto, C.N.
Quantum Mechanical Molecular Dynamics Approach to Study Charge Transfer.
In Kinetics and Dynamics, Paneth, P.; Dybala-Defratyka, A., Eds. Springer Netherlands: 2010; Vol. 12, pp 247-266.
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Anisimov, V.M., Bugaenko, V.L. and Cavasotto, C.N.
Quantum mechanical dynamics of charge transfer in ubiquitin in aqueous solution.
ChemPhysChem 10:3194-3196 (2009).
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Diaz, P., Phatak, S.S., Xu, J., Fronczek, F., Astruc-Diaz, F., Thompson, C., Cavasotto, C.N. and Naguib, M.
2,3-Dihydro-1-benzofuran Derivatives as a Novel Series of Potent Selective Cannabinoid Receptor 2 Agonists: Design, Synthesis, and Binding Mode Prediction through Ligand-steered Modeling,
ChemMedChem 4:1615-1629 (2009). Featured on cover page.
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Phatak, S.S., Stephan, C.C. and Cavasotto, C.N.
High-throughput and in silico screenings in drug discovery.
Expert Opin. Drug Discov. 4:947-959 (2009).
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Ziemys, A., Ferrari, M. and Cavasotto, C.N.
Molecular modeling of glucose diffusivity in silica nanochannels.
J. Nanosci. Nanotechnol. 9:6349-6359 (2009).
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Cavasotto, C.N. and Phatak, S.S.
Homology modeling in drug discovery: current trends and applications.
Drug Discov. Today 14:676-683 (2009).
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Diaz, P.; Phatak, S.; Xu, J.; Diaz, F-A.; Cavasotto, C.N. and Naguib, M.
6-Methoxy-N-alkyl Isatin Acylhydrazone Derivatives as a Novel Series of Potent Selective Cannabinoid Receptor 2 Inverse Agonists: Design, Synthesis, and Binding Mode Prediction.
J. Med. Chem. 52:433-444 (2009).
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Monti, M.C.; Casapullo, A.; Cavasotto, C.N.; Tosco, A.; Dal Piaz, F.; Ziemys, A.; Margarucci, L.; Riccio, R.
The binding mode of petrosaspongiolide M to the human group IIA phospholipase A(2): exploring the role of covalent and noncovalent interactions in the inhibition process.
Chem. Eur. J. 15:1155-1163 (2009).
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Bisson, W.H.; Abagyan, R. and Cavasotto, C.N.
Molecular Basis of Agonicity and Antagonicity in the Androgen Receptor Studied by Molecular Dynamics Simulations.
J. Mol. Graph. Mod. 27:452-458 (2008).
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Cavasotto, C.N. and Singh, N.
Docking and High-Throughput Docking: Successes and the challenge of protein flexibility.
Curr. Comput-Aided Drug Des. 4:221-234 (2008).
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Pineda Torra, I.; Ismaili, N.; Feig, J.E.; Xu, C.; Cavasotto, C.N.; Pancratov R.; Rogatsky, I.; Neubert, T.A.; Fisher, E.A. and Garabedian, M.J.
Phosphorylation of liver X receptor _ selectively regulates target gene expression in macrophages.
Mol. Cell. Biol. 28:2626-2636 (2008).
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Chen, W.; Dang, T.; Blind, R.D.; Wang, Z.; Cavasotto, C.N.; Hittelman, A.B.; Rogatsky, I.; Logan, S.K.; Garabedian, M.J.
Glucocorticoid receptor phosphorylation differentially affects target gene expression.
Mol. Endocrin. 22:1754-1766 (2008).
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Cavasotto, C.N.; Orry, A.J.W.; Murgolo, N.J.; Czarniecki, M.F.; Kocs, S.A.; Hawes, B.E.; O'Neill, K.A.; Hine, H.; Burton, M.S.; Voigt, J.H.; Bayne, M.L.; Monsma, F.J.
Discovery of Novel Antagonist Chemotypes to a G-Protein Coupled Receptor through Ligand-steered Homology Modeling and Structure-based Virtual Screening.
J. Med. Chem. 51:581-588 (2008).
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Monti, M.C.; Casapullo, A.; Cavasotto, C.N.; Napolitano, A. and Riccio, R.
Scalaradial, a dialdehyde-containing marine metabolite, exerts an unpredicted non-covalent PLA2 inactivation.
ChemBioChem 8:1585-1591 (2007).
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Cavasotto, C.N. and A.J.W. Orry.
Ligand Docking and Structure-based Virtual Screening in Drug Discovery.
Curr. Topics Med. Chem. 7:1006-1014 (2007).
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Cavasotto, C.N.; Ortiz, M.A.; Abagyan, R.; and Piedrafita, F.J.
In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells.
Bioorg. Med. Chem. Lett. 16:1969-1974 (2006).
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Cavasotto, C.N.
Ligand Docking and Virtual Screening in Structure-based Drug Discovery.
AIP Conf. Proc. 851:34-49 (2006).
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Orry, A.J.W.; Abagyan, R. and Cavasotto, C.N.
Structure-Based Development of Drug Target-Specific Compound libraries.
Drug Discov. Today 11:261-266 (2006).
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Cavasotto, C.N.; Orry, A.J.W. and Abagyan, R.
Receptor Flexibility in Ligand Docking.
In Handbook of Theoretical and Computational Nanotechnology, American Scientific Publishers. Eds. Michael Rieth and Wolfram Schommers, pp. 218-257 (2006).
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Hernández, J.A.; Meier, J.; Barrera, F.N.; Ruiz de los Paños, O.; Hurtado-Gómez, E.; Bes, M.T.; Fillat, M.T.; Peleato, M.L.; Cavasotto, C.N. and Neira, J.L.
The conformational stability and thermodynamics of Fur A (ferric uptake regulator) from Anabaena sp. PCC 7119.
Biophys. J. 89:4188-4200 (2005).
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Kovacs J.A., Cavasotto, C.N.; and Abagyan, R.A.
Conformational Sampling of Protein Flexibility in Generalized Coordinates: Aplication to ligand docking.
J. Comp. Theor. Nanosci. 2:354-361 (2005).
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Cavasotto, C.N.; Kovacs J.A. and Abagyan, R.A.
Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes.
J. Am. Chem. Soc. 127:9632-9640 (2005).
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Cavasotto, C.N.; Orry, A.J.W. and Abagyan, R.
The Challenge of Considering Rreceptor Flexibility in Ligand Docking and Virtual Screening.
Curr. Comput.-Aided Drug Des. 1:423-440 (2005).
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Li, W.; Cavasotto, C.N.; Cardozo, T.; Ha, S.; Dang, T.; Taneja, S.S.; Logan, S.K. and Garabedian, M.J.
Androgen receptor mutations identified in prostate cancer and androgen insensitivity syndrome display aberrant ART-27 coactivator function.
Mol. Endocrinol, 19: 2273-2282 (2005). (Featured on cover page of issue).
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Cavasotto, C.N. and Abagyan, R.
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases.
J. Mol. Biol. 337:209-225 (2004).
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Cavasotto, C.N.; Liu, G.; James, S. Y.; Hobbs, P. J.; Peterson, V. J.; Bhattacharya, A. A.; Kolluri, S. K.; Zhang, X.-K.; Leid, M.; Abagyan, R.; Liddington, R. C. and Dawson, M. I.
Determinants of Retinoid X Receptor Transcriptional Antagonism.
J. Med. Chem. 47:4360-4372 (2004).
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Bordner, A.J.; Cavasotto, C.N. and Abagyan, R.A.
Direct Derivation of Van der Waals Force Field Parameters from Quantum Mechanical Interaction Energies.
J. Phys. Chem. B. 107: 9601-9609 (2003)
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Cavasotto, C.N.; Orry, A.J.W. and Abagyan, R.A.
Structure-Based Identification of Binding Sites, Native Ligands and Potential Inhibitors for G-Protein Coupled Receptors.
Proteins: Structure, Function and Genetics, 51:423-433 (2003).
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Giribet, C.G.; Ruiz de Azúa, M.C.; Vizioli, C.V. and Cavasotto, C.N.
Electronic mechanisms of intra and intermolecular J couplings in systems with C-H…O interactions.
Int. J. Mol. Sci. 4: 203-217 (2003).
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Bordner, A.J.; Cavasotto, C.N. and Abagyan, R.A.
Calculation of water, n-octanol and n-hexadecane solvation free energies using a continuum electrostatics model.
J. Phys. Chem. B, 106:11009-11015 (2002).
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Cavasotto, C.N.
Finite expansion of the inverse matrix in the polarization propagator method.
Theor. Chem. Acc. 104: 491-498 (2000).
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Cavasotto, C.N. and Grinberg H.
A Liouville-space method for the decoupling of the polarization propagator equation of motion.
Chem. Phys. Lett. 303: 558-566 (1999).
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Bochicchio, R.; Ferraro, M.; Grinberg, H. and Cavasotto, C.
Self-energies for the particle-hole propagator from Feynman-Dyson equations.
J. Mol. Struct. (THEOCHEM) 335: 1-9, (1995).
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Cavasotto, C.N.; Giribet, C.G.; Ruiz de Azúa, M.C. and Contreras, R.H.
Exo-exo and endo-endo vicinal proton spin-spin coupling constants in norbornane and norbornene. An IPPP-CLOPPA analysis.
J. Comp. Chem. 12: 141-146 (1991).
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Cavasotto, C.N.; Giribet, C.G.; and Contreras, R.H.
Localization method for semiempirical molecular orbitals based of the Boys-Foster criterion.
J. Mol. Struct. (THEOCHEM) 210: 107-110 (1990).
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Contreras, R.H.; Giribet, C.G.; Ruiz de Azúa, M.C.; Cavasotto, C.N.; Aucar, G.A. and Krivdin L.B.
Quantum chemical analysis of the orientational lone-pair effect on spin-spin coupling constants.
J. Mol. Struct. (THEOCHEM) 210: 175-186 (1990).
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Cavasotto, C.N.; Giribet, C.G.; Ruiz de Azúa, M.C.; Contreras, R.H. and Pérez, J.
2J(Se-Se) couplings in diseleno-substituted alkenylic compounds: A CLOPPA-IPPP analysis.
J. Magn. Res. 87: 209-219 (1990).
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