Recent Publications

Reviews

•  ö  Abel, R.; Wang, L.; Mobley, D.L.; Friesner, R., "A Critical Review of Validation, Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations," Curr Top Med Chem., 2017, 17, 1-9

•  ö  Bhachoo, J. and Beuming, T., "Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite," Methods Mol Biol., 2017, 1561, 235-254

•  Sellers, B.D.; James, N.C.; Gobbi, A., "A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Drug-like Fragments," J. Chem. Inf. Model., 2017, 57 (6), 1265–1275

•  Ban, F., et al., "Best Practices of Computer-Aided Drug Discovery: Lessons Learned from the Development of a Preclinical Candidate for Prostate Cancer with a New Mechanism of Action," J. Chem. Inf. Model., 2017, 57(5), 1018–1028


Applications

•  ö  Kuhn, B., et al., "Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors," J. Med. Chem., 2017, 60 (6), 2485–2497

•  ö   Steinbrecher, T., et al., "Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability--Large-Scale Validation of MD-Based Relative Free Energy Calculations," J. Mol. Biol. , 2017, 429 (7), 948-963

•  ö   Steinbrecher, T.; Abel, R.; Clark, A.; Friesner, R., "Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutation," J. Mol. Biol. , 2017, 429 (7), 923–929

•  ö   Cappel, D.; Sherman, W.; Beuming, T., "Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery,"  Curr Top Med Chem., 2017, 17 (23), 2586-2598

•  ö   Krishnendu, P., et al., "Multifaceted Peptide Assisted One-Pot Synthesis of Gold Nanoparticles for Plectin-1 Targeted Gemcitabine Delivery in Pancreatic Cancer," Nanoscale, 2017, 9, 15622-15634

•  Zaccagnini, L., et al., "Identification of Novel Fluorescent Probes Preventing PrPSc Replication in Prion Diseases," European Journal of Medicinal Chemistry, 2017, 127 (15), 859–873

•  Chemi, G., et al., "Computational Tool for Fast In silico Evaluation of hERG K+ Channel Affinity," Front. Chem. , 2017, 5 (7), 1-9

•  Van Den Driessche, G. and Fourches, D., "Adverse Drug Reactions Triggered by the Common HLA-B*57:01 Variant: A Molecular Docking Study," J. Cheminform., 2017, 9 (13), 1-17

•  Ash, J. and Fourches, D., "Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories," J. Chem. Inf. Model., 2017, 57 (6), 1286–1299


Methods Development

•  ö   Shelley, M.Y., et al., "A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution," J. Chem. Theory Comput., 2017, 13 (8), 3881–3897

•  ö   Sindhikara, D., et al., "Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling," J. Chem. Inf. Model., 2017, 57 (8), 1881–1894