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· publication by Schrödinger author

·Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Dilek Coskun, Muyun Lihan, Joao Rodrigues, Marton Vass, Daniel Robinson, Richard Friesner, Edward Miller

ChemRxiv Theoretical and Computational Chemistry, 2023, PreprintView

Small Molecule Drug Discovery

·OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

Roos, K.; Wu, C.; Damm, W.; Reboul, M.; Stevenson, J.M.; Lu, C.; Dahlgren, M.K.; Mondal, S.; Chen, W.; Wang, L.; Abel, R.; Friesner, R.A.; Harder, E.D.

J. Chem. Theory Comput., 2019, 1863–1874View

Small Molecule Drug Discovery

·Modeling the value of predictive affinity scoring in preclinical drug discovery

Abel, R., Manas, E.S., Friesner, R.A., Farid, R.S., Wang, L.

Curr Opin Struct Biol., 2018, DOI: 10.1016/j.sbi.2018.09.002View

Small Molecule Drug Discovery

·Investigating Protein–Peptide Interactions Using the Schrödinger Computational Suite

Bhachoo, J.; Beuming, T.

Methods Mol Biol., 2017, 1561, 235-254View

Small Molecule Drug Discovery

·Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations

Steinbrecher, T.; Zhu, C.; Wang, L.; Abel, A.; Negron, C.; Pealman, D.; Feyfant, E.; Duan, J.; Sherman, W.

J. Mol. Biol. , 2017, 429 (7), 948-963View

Small Molecule Drug Discovery

·Relative Binding Free Energy Calculations Applied to Protein Homology Models

Cappel, D.; Hall, M.L.; Lenselink, E.B.; Beuming, T.; Qi, J.; Bradner, J.; Sherman, W.

J. Chem. Inf. Model., 2016, 56 (12), 2388–2400View

Small Molecule Drug Discovery

·Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition

Leung, S. S. F., Sindhikara, D. J., and Jacobson, M. P.

J. Chem. Inf. Model., 2016, 56(5), 924–929View

Small Molecule Drug Discovery

·OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J.Y.; Wang, L.; Lupyan, D.; Dahlgren, M.K.; Knight, J.L.; Kaus, J.W.; Cerutti, D.S.; Krilov, G.; Jorgensen, W.L.; Abel, R.; Friesner, R.A.

J. Chem. Theory Comput., 2016, 2 (1), 281–296View

Small Molecule Drug Discovery

Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1

Chrencik, J.E.; Roth, C.B.; Terakado, M.; Kurata, H.; Omi, R.; Kihara, Y.; Warshaviak, D.; Nakade, S.; Asmar-Rovira, G.; Mileni, M.; Mizuno, H.; Griffith, M.T.; Rodgers, C.; Han, G.W.; Velasquez, J.; Chun, J.; Stevens, R.C.; Hanson, M.A.

Cell, 2015, 161(7), 1633-1643View

Small Molecule Drug Discovery

·Chemical Basis for the Recognition of Trimethyllysine by Epigenetic Reader Proteins

Kamps, J.J.A.G.; Huang, J.; Poater, J.; Xu, C.; Pieters, B.J.G.E.; Dong, A.; Min, M.; Sherman, W.; Beuming, T.; Bickelhaupt, F.M.; Li, H.; Mecinović, J.

Nat. Commun., 2015, 6, doi:10.1038/ncomms9911View

Small Molecule Drug Discovery

·Exploring Conformational Search Protocols for Ligand-based Virtual Screening and 3-D QSAR Modeling

Cappel, D.; Dixon, S.L.; Sherman, W.; Duan, J.

J. Comput. Aided Mol. Des., 2015, 29(2), 165-182View

Small Molecule Drug Discovery

·On the Rational Design of Zeolite Clusters

Migues, A.N.; Muskat, A.; Auerbach, S.M.; Sherman, W.; Vaitheeswaran, S.

ACS Catal., 2015, 5, 2859-2865View

Small Molecule Drug Discovery

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