Chemistry Reference
In-Depth Information
[130] Diaz P, Phatak SS, Xu J, Fronczek FR, Astruc-Diaz F. Thompson CM, Cavasotto CN,
Naguib M. 2,3-Dihydro-1- benzofuran derivatives as a series of potent selective
cannabinoid receptor 2 agonists: design, synthesis, and binding mode prediction through
ligand-steered modeling. Chem Med Chem, 2009, 4: 1615-1629.
[131] Lin MS, Head-Gordon T. Reliable protein structure refinement using a physical energy
function. J. Comput. Chem., 2011, 32: 709-717.
[132] Cavasotto CN, Kovacs JA, Abagyan RA. Representing Receptor Flexibility in Ligand
Docking through Relevant Normal Modes. J. Am. Chem. Soc., 2005, 127: 9632-9640.
[133] Kovacs JA, Cavasotto CN, Abagyan RA. Conformational Sampling of Protein Flexibility
in Generalized Coordinates: Application to ligand docking. J. Comp. Theor. Nanosci, 2005,
2: 354- 361.
[134] Rai BK, Tawa GJ, Katz AH. Humblet C. Modeling G protein-coupled receptors for
structure-based drug discovery using low-frequency normal modes for refinement of
homology models: application to H3 antagonists. Proteins, 2010, 78: 457-473.
[135] Sperandio O, Mouawad L, Pinto E, Villoutreix BO, Perahia D, Miteva MA. How to choose
relevant multiple receptor conformations for virtual screening: a test case of CDK2 and
normal mode analysis. Eur. Biophys. J., 2010, 39: 1365-1372.
[136] Cavasotto CN, Abagyan RA. Protein flexibility in ligand dock-ing and virtual screening to
protein kinases. J. Mol. Biol., 2004, 337: 209-225.
[137] Cavasotto CN, Liu G, James SY, Hobbs PD, Peterson VJ, Bhattacharya AA, Kolluri S K,
Zhang XK, Leid M, Abagyan R, Liddington RC, Dawson MI. Determinants of retinoid X
receptor transcriptional antagonism. J. Med. Chem., 2004, 47: 4360-4372.
[138] Monti MC, Casapullo A, Cavasotto CN, Napolitano A, Riccio R. Scalaradial, a dialdehyde-
containing marine metabolite that causes an unexpected noncovalent PLa(2) inactivation.
ChemBioChem, 2007, 8: 1585-1591.
[139] Monti MC, Casapullo A, Cavasotto CN, 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. 2009, 15: 1155-1163.
[140] Vilar S, Ferino G, Phatak SS, Berk B, Cavasotto CN, Costanzi S. Docking-based virtual
screening for GPCRs ligands: not only crystal structures but also
in silico
models. J. Mol.
Graph. Model. 2011, 29: 614-623.
[141] Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Schoichet BK, Sali A, Statistical
potential for modeling and ranking of protein-ligand interactions, J. Chem. Inf. Mol, 2011,
51: 3078-3092.
[142] Garcia-Sosa AT, Hetenyl C, Maran U, Drug efficiency indices for improvement of
molecular docking scoring functions, J. Comput. Chem, 2011,31: 174-184.
[143] Bordogna A, Pandini A, Bonati L, Predicting the accuracy of protein-ligand docking on
homology models, J. Comput. Chem. 2011, 32: 81-98.
[144] Obiol-Pardo, Lopez L, Pastor M, Selent J, Progress in the structural prediction of G
protein-coupled receptors:D
3
receptor in complex with eticlopride, Proteins, 2011, 79:1695-
17703.
[145] Phatak SS, Gatica EA, Cavasotto CN, Ligand-steered modeling and docking a
benchmarking study in class a G-protein-coupled receptors, J. Chem. Inf. Model, 2010,
50:2119-2128.
