title: Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite.
abstract: The Schrödinger software suite contains a broad array of computational chemistry and molecular modeling tools that can be used to study the interaction of peptides with proteins. These include molecular docking using Glide and Piper, relative binding free energy predictions with FEP+, conformational searches using MacroModel and Desmond, and structural refinement using Prime and PrimeX. In this review we provide a comprehensive overview of these tools and describe their potential application in the identification and optimization of peptide ligands for proteins.
authors.affiliation: Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, NY, 10036, USA.
authors.forename: Jas
authors.initials: J
authors.lastname: Bhachoo
authors.affiliation: Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, NY, 10036, USA. thijs.beuming@schrodinger.com.
authors.forename: Thijs
authors.initials: T
authors.lastname: Beuming
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: Conformational search; Docking; Free Energy; Glide; Molecular dynamics; Peptides; Piper; Prime; Protein refinement