• •  ö  Tran, Q.T.; Williams, S.; Farid, R.; Erdemli, G.; Pearlstein, R., "The translocation kinetics of antibiotics through porin OmpC: Insights from structure-based solvation mapping using watermap ," Proteins, 2012, in press
• •  ö  Myrianthopoulos, V.; Kritsanida, M.; Gaboriaud-Kolar, N.; Magiatis, P.; Ferandin, Y.; Durieu, E.; Lozach, O.; Cappel, D.; Soundararajan M; Filippakopoulos P; Sherman W; Knapp S; Meijer L; Mikros E; Skaltsounis AL, "Novel inverse binding mode of indirubin derivatives yields improved selectivity for DYRK kinases," ACS Med Chem Lett, 2012, in press
• •  Brodney, M. A.; Barreiro, G.; Ogilvie, K.; Hajos-Korcsok, E.; Murray, J.; Vajdos, F.; Ambroise, C.; Christoffersen, C.; Fisher, K.; Lanyon, L.; Liu, J.; Nolan, C. E.; Withka, J. M.; Borzilleri, K. A.; Efremov, I.; Oborski, C. E.; Varghese, A.; O'Neill, B, "Spirocyclic Sulfamides as BACE-1 Inhibitors for the Treatment of Alzheimer's Disease: Utilization of Structure Based Drug Design, WaterMap, and CNS Penetration Studies to Identify Centrally Efficacious Inhibitors," J Med Chem., 2012, 55, 9224-39
• •  ö  Newman, A.H.; Beuming, T.; Banala, A.K.; Donthamsetti, P.; Pongetti, K.; LaBounty, A.; Levy, B.; Cao, J.; Michino, M.; Luedtke, R.P.; Javitch, J.A.; Shi, L., "Molecular determinants of selectivity and efficacy at the dopamine D3 receptor," J. Med. Chem., 2012, 55 (15), 6689–6699
• •  ö  Shah, F.; Jiri, G.; Legac, J.; Shivakumar, D.; Sherman, W.; Rosenthal, P.; Avery, M., "Computer-aided drug design of falcipain inhibitors: Virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis," J. Chem. Inf. Model., 2011, 52, 696-710
• •  ö  Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W., "Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization," Proteins, 2011, 80, 871-83
• •  ö  Snyder. P.W.; Mecinovic, J.; Moustakas, D.; Thomas, S, III.; Harder, M.l.; Mack, E.; Lockett, M.; Héroux, A.; Sherman, W.; Whitesides, G., "Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase," PNAS, 2011, 108, 17889-17894
• •  ö  Abel, R.; Salam, N.K.; Shelley, J.; Farid, R.; Friesner, R.A.; 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, 6, 1049-1066
• •  Charrier, J. D.; Miller, A.; Kay, D. P.; Brenchley, G.; Twin, H. C.; Collier, P. N.; Ramaya, S.; Keily, S. B.; Durrant, S. J.; Knegtel, R. M.; et. al. , "Discovery and structure-activity relationship of 3-aminopyrid-2-ones as potent and selective interleukin-2 inducible T-cell kinase (Itk) inhibitors," J. Med. Chem. 2011, 54, 2341-2350. , 2011, 54, 2341-2350
• •  Knegtel R. M. A.; Robinson, D. D. , "A role for hydration in interleukin-2 inducible T-cell kinase (Itk) selectivity," Mol. Inf. 2011, 30, 950–959., 2011, 30, 950–959
• •  Ohno, K.; Mori, K.; Orita, M.; Takeuchi, M. , "Computational Insights into Binding of Bisphosphates to Farnesyl Pyrophosphate Synthase," Curr. Med. Chem., 2011, 18, 220-233
• •  Pellicciari, R.; Camaioni, E.; Gilbert, A. M.; Macchiarulo, A.; Bikker, J. A.; Shah, F.; Bard, J.; Costantino, G.; Gioiello, A.; Robertson, G. M.; et. al. , "Discovery and characterization of novel potent PARP-1 inhibitors endowed with neuroprotective properties: From TIQ-A to HYDAMTIQ," Med. Chem. Commun., 2011, 2, 559-565
• •  ö  Wang, L.; Berne, B. J.; Friesner R. A., "Ligand binding to protein-binding pockets with wet and dry regions," Proc. Natl. Acad. Sci. U S A., 2011, 108, 1326-30
• •  ö  Abel, R.; Wang, L.; Friesner, R. A.; Berne, B. J. , "A displaced-solvent functional analysis of model hydrophobic enclosures," J. Chem. Theory Comput. , 2010, 6, 2924-2934
• •  Chrencik, J.E.; Patny, A.; Leung, I. K.; Korniski, B.; Emmons, T.L.; Hall, T.; Weinberg, R.A.; Gormley, J.A, Williams, J.M.; Day, J. E.; et al. , "Structural and thermodynamic characterization of the TYK2 and JAK3 kinase domains in complex with CP-690550 and CMP-6.," J. Mol. Biol., 2010, 400, 413-433
• •  Guimarães, C. R.; Mathiowetz, A. M. , "Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations," J. Chem. Inf. Model., 2010, 50, 547-559
• •  Han, S.; Zaniewski, R. P.; Marr, E. S.; Lacey, B. M.; Tomaras, A. P.; Evdokimov, A.; Miller, J. R.; Shanmugasundaram, V. , "Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa.," Proc. Natl. Acad. Sci. U S A. , 2010, 107, 22002-7
• •  ö  Higgs, C.; Beuming, T.; Sherman W. , "Hydration site thermodynamics explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor," ACS Med. Chem. Lett., 2010, 1, 160-164
• •  Huggins, D. J.; McKenzie, G. J.; Robinson D. D.; Narváez, A. J.; Hardwick, B.; Roberts-Thomson, M.; Venkitaraman, A. R.; Grant, G. H.; Payne, M. C. , "Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation," PLoS Comput. Biol., 2010, 8, e1000880
• •  ö  Pearlstein, R. A.; Hu, Q. Y.; Zhou, J.; Yowe, D.; Levell, J.; Dale, B.; Kaushik, V. K.; 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, 78, 2571–2586
• •  ö  Robinson, D. D.; Sherman, W.; Farid, R., "Understanding kinase selectivity through energetic analysis of binding site waters," Chem. Med. Chem., 2010, 5, 618– 627
• •  ö  Beuming, T.; Farid, R.; Sherman W. , "High-energy water sites determine peptide binding affinity and specificity of PDZ domains," Protein Sci., 2009, 8, 1609-1619
• •  Clausen, R. P.; Naur, P.; Kristensen, A. S.; Greenwood, J. R.; Strange, M.; Bräuner-Osborne, H.; Jensen, A. A.; Nielsen, A. S.; Geneser, U.; Ringgaard, L. M.; et.al., "The glutamate receptor GluR5 agonist (S)-2-amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic acid and the 8-methyl analogue: synthesis, molecular pharmacology, and biostructural characterization," J. Med. Chem., 2009, 52, 4911-4922
• •  ö  Wang, L.; Abel, R.; Friesner, R.; Berne, B. J., "Thermodynamic Properties of Liquid Water: An Application of a Nonparametric Approach to Computing the Entropy of a Neat Fluid," J. Chem. Theory Comput. , 2009, 5, 1462-1473
• •  ö  Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A., "Role of the active-site solvent in the thermodynamics of Factor Xa ligand binding," J. Am. Chem Soc., 2008, 9, 2817-31
• •  ö  Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. , "Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding," Proc. Natl. Acad. Sci. U S A., 2007, 104, 808-813

• ö indicates papers (co)authored by Schrödinger scientist(s).