• 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).
  • 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).
  • 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.
  • 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.
  • Cavasotto, C.N.
    Normal-mode-based approaches in receptor ensemble docking.
    Methods Mol. Biol. 819:157-168 (2012).
  • Echenique P., Cavasotto, C.N., García-Risueño, P.
    The canonical equilibrium of constrained molecular models.
    Eur. Phys. J. ST, 200:5-54, (2011)
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • Cavasotto, C.N.
    Homology models in docking and high-throughput docking.
    Curr. Top. Med. Chem. 11:1528-1534 (2011).
  • 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).
  • Cavasotto, C.N. and Phatak S.S.
    Docking Methods for Structure-based Library Design.
    Methods Mol. Biol. 685:155-174 (2011).
  • 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.
  • 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).
  • 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.
  • 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).
  • 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.
  • 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).
  • Ziemys, A., Ferrari, M. and Cavasotto, C.N.
    Molecular modeling of glucose diffusivity in silica nanochannels.
    J. Nanosci. Nanotechnol. 9:6349-6359 (2009).
  • Cavasotto, C.N. and Phatak, S.S.
    Homology modeling in drug discovery: current trends and applications.
    Drug Discov. Today 14:676-683 (2009).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • Cavasotto, C.N.
    Ligand Docking and Virtual Screening in Structure-based Drug Discovery.
    AIP Conf. Proc. 851:34-49 (2006).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • Cavasotto, C.N. and Abagyan, R.
    Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases.
    J. Mol. Biol. 337:209-225 (2004).
  • 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).
  • 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)
  • 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).
  • 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).
  • 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).
  • Cavasotto, C.N.
    Finite expansion of the inverse matrix in the polarization propagator method.
    Theor. Chem. Acc. 104: 491-498 (2000).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).