Woody Sherman
Woody Sherman
Silicon Therapeutics
Verifierad e-postadress på silicontx.com - Startsida
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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
GM Sastry, M Adzhigirey, T Day, R Annabhimoju, W Sherman
Journal of computer-aided molecular design 27 (3), 221-234, 2013
19252013
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
14012006
Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field
D Shivakumar, J Williams, Y Wu, W Damm, J Shelley, W Sherman
Journal of chemical theory and computation 6 (5), 1509-1519, 2010
8872010
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field
L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ...
Journal of the American Chemical Society 137 (7), 2695-2703, 2015
5742015
Use of an induced fit receptor structure in virtual screening
W Sherman, HS Beard, R Farid
Chemical biology & drug design 67 (1), 83-84, 2006
3942006
Probing the α‐helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis
Z Guo, U Mohanty, J Noehre, TK Sawyer, W Sherman, G Krilov
Chemical biology & drug design 75 (4), 348-359, 2010
3552010
ConfGen: a conformational search method for efficient generation of bioactive conformers
KS Watts, P Dalal, RB Murphy, W Sherman, RA Friesner, JC Shelley
Journal of chemical information and modeling 50 (4), 534-546, 2010
3112010
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
PW Snyder, J Mecinović, DT Moustakas, SW Thomas, M Harder, ET Mack, ...
Proceedings of the National Academy of Sciences 108 (44), 17889-17894, 2011
2942011
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods
J Duan, SL Dixon, JF Lowrie, W Sherman
Journal of Molecular Graphics and Modelling 29 (2), 157-170, 2010
2812010
Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments
M Sastry, JF Lowrie, SL Dixon, W Sherman
Journal of chemical information and modeling 50 (5), 771-784, 2010
2602010
Water networks contribute to enthalpy/entropy compensation in protein–ligand binding
B Breiten, MR Lockett, W Sherman, S Fujita, M Al-Sayah, H Lange, ...
Journal of the American Chemical Society 135 (41), 15579-15584, 2013
2532013
Novel method for generating structure-based pharmacophores using energetic analysis
NK Salam, R Nuti, W Sherman
Journal of chemical information and modeling 49 (10), 2356-2368, 2009
2262009
Rational approaches to improving selectivity in drug design
DJ Huggins, W Sherman, B Tidor
Journal of medicinal chemistry 55 (4), 1424-1444, 2012
2232012
Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design
LA Clark, PA Boriack‐Sjodin, J Eldredge, C Fitch, B Friedman, KJM Hanf, ...
Protein science 15 (5), 949-960, 2006
1742006
Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring
GM Sastry, SL Dixon, W Sherman
Journal of chemical information and modeling 51 (10), 2455-2466, 2011
1492011
Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Z Cournia, B Allen, W Sherman
Journal of chemical information and modeling 57 (12), 2911-2937, 2017
1462017
Improving the prediction of absolute solvation free energies using the next generation OPLS force field
D Shivakumar, E Harder, W Damm, RA Friesner, W Sherman
Journal of chemical theory and computation 8 (8), 2553-2558, 2012
1382012
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
K Loving, NK Salam, W Sherman
Journal of computer-aided molecular design 23 (8), 541-554, 2009
1362009
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
T Beuming, Y Che, R Abel, B Kim, V Shanmugasundaram, W Sherman
Proteins: Structure, Function, and Bioinformatics 80 (3), 871-883, 2012
1342012
Modeling local structural rearrangements using FEP/REST: application to relative binding affinity predictions of CDK2 inhibitors
L Wang, Y Deng, JL Knight, Y Wu, B Kim, W Sherman, JC Shelley, T Lin, ...
Journal of chemical theory and computation 9 (2), 1282-1293, 2013
1322013
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