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· publication by Schrödinger author
·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.
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.
Small Molecule Drug Discovery
·AutoQSAR: An Automated Machine Learning Tool for Best-Practice QSAR Modeling
Dixon, S.L.; Duan, J.; Smith, E.; Von Bargen, C.D.; Sherman, W.; Repasky, M.P.
Small Molecule Drug Discovery
·Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
Lenselink, E.B.; Louvel, J.; Forti, A.F.; van Veldhoven, J.P.D.; de Vries, H.; Mulder-Krieger, T.; McRobb, F.M.; Negri, A.; Goose, J.; Abel, R.; van Vlijmen, H.W.T.; Wang, L.; Harder, E.; Sherman, W.; IJzerman, A.P.; Beuming, T.
Small Molecule Drug Discovery
·Accurate Binding Free Energy Predictions in Fragment Optimization
Steinbrecher, T.B.; Dahlgren, M.; Cappel, D.; Lin, T.; Wang, L.; Krilov, G.; Abel, R.; Friesner, R.; Sherman, W.
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.
Small Molecule Drug Discovery
·Selection of Nanobodies that Block the Enzymatic and Cytotoxic Activities of the Binary Clostridium Difficile Toxin CDT
Unger, M; Eichhoff, AM; Schumacher, L; Strysio, M; Menzel, M; Schwan, C; Alzogaray, V; Zylberman, V; Seman, M; Brandner, J; Rohde, H; Zhu, K; Haag, F; Mittrücker, H; Goldbaum, F; Aktories, K; Koch-Nolte, F.
Biologics Drug Discovery
Optimization, Pharmacophore Modeling and 3D-QSAR Studies of Sipholanes as Breast Cancer Migration and Proliferation Inhibitors
Foudah, A.I.; Sallam, A.A.; Akl, M.R.; El Sayed, K.A.
Small Molecule Drug Discovery
The marine-derived sipholenol A-4-O-3′,4′-dichlorobenzoate inhibits breast cancer growth and motility in vitro and in vivo through the suppression of Brk and FAK signaling
Akl, M.R.; Foudah, A.I.; Ebrahim, H.Y.; Meyer, S.A.; El Sayed, K.A.
Small Molecule Drug Discovery
·A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring
Sirin, S.; Kumar, R.; Martinez, C.; Karmilowicz, M.J.; Ghosh, P.; Abramov, Y.A.; Martin, V.; Sherman, W.
Biologics Drug Discovery
·Physics-Based Enzyme Design: Predicting Binding Affinity and Catalytic Activity
Sirin, S.; Pearlman, D.A.; Sherman, W.
Small Molecule Drug Discovery
·Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase
Gannavaram, S.; Sirin, S.; Sherman, W.; Gadda, G.