Methods Development
Park, M.; Gao, C.; Stern, H.A., "Estimating binding affinities by docking/scoring methods using variable protonation states," Proteins, 2011, 79, 304-314.
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE, “Improved side-chain torsion potentials for the Amber ff99SB protein force field,” Proteins, 2010, 78, 1950-8.
Greenwood J, Calkins D, Sullivan A, Shelley J, “Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution,” J. Comput. Aided Mol. Des., 2010, 24, 591-604.
Gallicchio E, Lapelosa M, Levy RM, “Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Affinities,” J. Chem. Theory Comput., 2010, 6, 2961-2977.
Applications
Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W, "Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases," Chem. Med. Chem. 2011, ASAP.
Tanaka D, Tsuda Y, Shiyama T, Nishimura T, Chiyo N, Tominaga Y, Sawada N, Mimoto T, Kusunose N, “A Practical Use of Ligand Efficiency Indices Out of the Fragment-Based Approach: Ligand Efficiency-Guided Lead Identification of Soluble Epoxide Hydrolase Inhibitors,” J. Med. Chem., 2011, 54, 851-857.
Chu Y, Chen X, Yang Y, Tang Y, “Identification of small molecular inhibitors for Ero1p by structure-based virtual screening,” Bioorg. Med. Chem. Lett., 2011, 21, 1118-21.
Liu H, Walker LA, Nanayakkara NP, Doerksen RJ, “Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B's role in nitric oxide synthase,” J. Am. Chem. Soc., 2011, 133, 1172-5.
Sun X, Li Y, Li W, Xu Z, Tang Y, “Computational investigation of interactions between human H2 receptor and its agonists,” J. Mol. Graph. Model., 2011, 29, 693-701.
Szatkowski L, Thompson MK, Kaminski R, Franzen S, Dybala-Defratyka, “Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: Horseradish peroxidase and dehaloperoxidase,” Arch. Biochem. Biophys., 2011, 505, 22-32.
Unwalla RJ, Cross JB, Salaniwal S, Shilling AD, Leung L, Kao J, Humblet C, “Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism,” J. Comput. Aided Mol. Des., 2010, 24, 237-56.
Li X, Li Y, Cheng T, Liu Z, Wang R, “Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes,” J. Comput. Chem., 2010, 31, 2109-25.
Pearlstein RA, Hu QY, Zhou J, Yowe D, Levell J, Dale B, Kaushik VK, Daniels D, Hanrahan S, Sherman W, Abel R, “New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor-like repeat A docking site using WaterMap,” Proteins, 2010, 12, 2571.
Abel R, Wang L, Friesner RA, Bern BJ, “A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures,” J. Chem. Theory. Comput., 2010, 6, 2924-293.