| Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments G Madhavi Sastry, M Adzhigirey, T Day, R Annabhimoju, W Sherman Journal of computer-aided molecular design 27, 221-234, 2013 | 5512 | 2013 |
| A hierarchical approach to all‐atom protein loop prediction MP Jacobson, DL Pincus, CS Rapp, TJF Day, B Honig, DE Shaw, ... Proteins: Structure, Function, and Bioinformatics 55 (2), 351-367, 2004 | 2480 | 2004 |
| Novel procedure for modeling ligand/receptor induced fit effects W Sherman, T Day, MP Jacobson, RA Friesner, R Farid Journal of medicinal chemistry 49 (2), 534-553, 2006 | 2138 | 2006 |
| New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies R Farid, T Day, RA Friesner, RA Pearlstein Bioorganic & medicinal chemistry 14 (9), 3160-3173, 2006 | 531 | 2006 |
| Docking covalent inhibitors: a parameter free approach to pose prediction and scoring K Zhu, KW Borrelli, JR Greenwood, T Day, R Abel, RS Farid, E Harder Journal of chemical information and modeling 54 (7), 1932-1940, 2014 | 436 | 2014 |
| A second generation multistate empirical valence bond model for proton transport in aqueous systems TJF Day, AV Soudackov, M Čuma, UW Schmitt, GA Voth The Journal of chemical physics 117 (12), 5839-5849, 2002 | 352 | 2002 |
| The hydrated proton at the water liquid/vapor interface MK Petersen, SS Iyengar, TJF Day, GA Voth The Journal of Physical Chemistry B 108 (39), 14804-14806, 2004 | 316 | 2004 |
| Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction K Zhu, T Day, D Warshaviak, C Murrett, R Friesner, D Pearlman Proteins: Structure, Function, and Bioinformatics 82 (8), 1646-1655, 2014 | 235 | 2014 |
| The mechanism of hydrated proton transport in water TJF Day, UW Schmitt, GA Voth Journal of the American Chemical Society 122 (48), 12027-12028, 2000 | 233 | 2000 |
| The properties of ion-water clusters. I. The protonated 21-water cluster SS Iyengar, MK Petersen, TJF Day, CJ Burnham, VE Teige, GA Voth The Journal of chemical physics 123 (8), 2005 | 207 | 2005 |
| On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study SS Iyengar, TJF Day, GA Voth International Journal of Mass Spectrometry 241 (2-3), 197-204, 2005 | 119 | 2005 |
| AggScore: prediction of aggregation‐prone regions in proteins based on the distribution of surface patches K Sankar, SR Krystek Jr, SM Carl, T Day, JKX Maier Proteins: Structure, Function, and Bioinformatics 86 (11), 1147-1156, 2018 | 115 | 2018 |
| The properties of ion-water clusters. II. Solvation structures of Na+, Cl−, and H+ clusters as a function of temperature CJ Burnham, MK Petersen, TJF Day, SS Iyengar, GA Voth The Journal of chemical physics 124 (2), 2006 | 113 | 2006 |
| Improving accuracy, diversity, and speed with prime macrocycle conformational sampling D Sindhikara, SA Spronk, T Day, K Borrelli, DL Cheney, SL Posy Journal of chemical information and modeling 57 (8), 1881-1894, 2017 | 112 | 2017 |
| Reliable and accurate solution to the induced fit docking problem for protein–ligand binding EB Miller, RB Murphy, D Sindhikara, KW Borrelli, MJ Grisewood, F Ranalli, ... Journal of Chemical Theory and Computation 17 (4), 2630-2639, 2021 | 107 | 2021 |
| Ion solvation dynamics in water–methanol and water–dimethylsulfoxide mixtures TJF Day, GN Patey The Journal of chemical physics 110 (22), 10937-10944, 1999 | 86 | 1999 |
| PrimeX and the Schrödinger computational chemistry suite of programs JA Bell, Y Cao, JR Gunn, T Day, E Gallicchio, Z Zhou, R Levy, R Farid International Union of Crystallography, 2012 | 61 | 2012 |
| Theory of ion solvation dynamics in mixed dipolar solvents A Yoshimori, TJF Day, GN Patey The Journal of chemical physics 109 (8), 3222-3231, 1998 | 61 | 1998 |
| qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps GCP van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ... Journal of Medicinal Chemistry 61 (24), 11183-11198, 2018 | 53 | 2018 |
| Ion solvation dynamics in binary mixtures TJF Day, GN Patey The Journal of chemical physics 106 (7), 2782-2791, 1997 | 51 | 1997 |
