Methods papers
Sandor M.; Kiss R.; Keseru G.M., "Virtual fragment docking by glide: A validation study on 190 protein-fragment complexes", J. Chem. Inf. Model., 2010, 50, 1165–1172
Duan J.; Dixon S.L.; Lowrie J.F.; Sherman W., "Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods", J. Mol. Graph. Model. , 2010, Article ASAP
Young T.; Hua L.; Huang X.; Abel R.; Friesner R. Berne B.J., "Dewetting transitions in protein cavities", Proteins, 2010, 78, 1856-69
Chen I.-J.; Foloppe N., "Drug-like bioactive structures and conformational coverage with the ligprep/confgen suite: Comparison to programs MOE and catalyst", J. Chem. Inf. Model., 2010, 50, 822-39
Brooijmans N.; Humblet C., "Chemical space sampling by different scoring functions and crystal structures", J. Comput. Aided Mol. Des., 2010, 24, 433-47
Applications: Computer-aided drug design
Jiao W.; McDonald D.Q.; Coxon J.M.; Parker E.J., "Molecular modeling studies of peptide inhibitors highlight the importance of conformational prearrangement for inhibition of calpain",
Biochemistry, 2010, 49, 5533-9
Alzate-Morales J.H.; Vergara-Jaque A.; Caballero J., "Computational study on the interaction of N1 substituted pyrazole derivatives with B-Raf kinase: An unusual water wire hydrogen-bond network and novel interactions at the entrance of the active site", J. Chem. Inf. Model., 2010, 50, 1101-12
Maruoka H.; Barrett M.O.; Ko H.; Tosh D.K.; Melman A.; Burianek L.E. et al., "Pyrimidine ribonucleotides with enhanced selectivity as P2Y6 receptor agonists: Novel 4-alkyloxyimino, (S)-methanocarba, and 5′-triphosphate γ-ester modifications", J. Med. Chem., 2010, 53, 4488-501
Tang J.; Maddali K.; Pommier Y.; Sham Y.Y.; Wang Z., "Scaffold rearrangement of dihydroxypyrimidine inhibitors of HIV integrase: Docking model revisited", Bioorg. Med. Chem. Lett., 2010, 20, 3275-9
Lopez-Ramos M.; Perruccio F., "HPPD: Ligand- and target-based virtual screening on a herbicide target",
J. Chem. Inf. Model., 2010, 23, 801-14
Kalyanaraman C.; Jacobson M.P., "Studying enzyme-substrate specificity in silico: A case study of the escherichia coli glycolysis pathway", Biochemistry, 2010, 49, 4003-5
Tsirkone V.G.; Tsoukala E.; Lamprakis C.; Manta S., Hayes J.M.; Skamnaki V.T. et al., "1-(3-Deoxy-3-fluoro-β-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies", Bioorg. Med. Chem., 2010
Ali S.T.; Jahangir S.; Karamat S.; Fabian W.M.F.; Nawara K.; Kona J., "Theoretical study on the redox cycle of bovine glutathione peroxidase GPx1: PKa calculations, docking, and molecular dynamics simulations", J. Chem. Theory Comput., 2010, 6, 1670-81
Georgiev V.; Noack H.; Borowski T.; Blomberg M.R.A.; Siegbahn P.E.M., "DFT study on the catalytic reactivity of a functional model complex for intradiol-cleaving dioxygenases",
J. Phys. Chem. B, 2010, 114, 5878-85
Chung J.Y.; Chung H.W.; Cho S.J.; Hah J.-M.; Cho A.E., "QM/MM based 3D QSAR models for potent B-Raf inhibitors", J. Comput. Aided Mol. Des., 2010, 24,385-97
Diaz N.; Suarez D.; Suarez E., "Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations", Proteins, 2010, 78, 1-11
Tawari N.R.; Degani M.S., "Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity", J. Comput. Chem., 2010, 31, 739-51
Shen J.; Tan C.; Zhang Y.; Li X.; Li W.; Huang J. et al., "Discovery of Potent Ligands for Estrogen Receptor β by Structure-Based Virtual Screening", J. Med. Chem., 2010, 53, 5361-5
Liao C.; Park J.-E.; Bang J.K.; Nickalus M.C.; Lee K.S., "Probing Binding Modes of Small Molecule Inhibitors to the Polo-Box Domain of Human Polo-like Kinase 1", ACS Med. Chem. Lett., 2010, 1, 110-114