title: OSPREY: protein design with ensembles, flexibility, and provable algorithms.
abstract: We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling of proteins and ligands as ensembles of low-energy structures to better approximate binding affinity; and (3) a globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect to the input model. Here, we illustrate the importance of these three characteristics. We then describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been used prospectively, with experimental validation, in several biomedically relevant settings. We show in detail how OSPREY has been used to predict resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application.
  
  
  BACKGROUND
  OSPREY is free and open source under a Lesser GPL license. The latest version is OSPREY 2.0. The program, user manual, and source code are available at www.cs.duke.edu/donaldlab/software.php.
  
  
  BACKGROUND
  osprey@cs.duke.edu.
authors: Department of Computer Science, Duke University, Durham, North Carolina, USA.
authors: Pablo
authors: P
authors: Gainza
authors: Kyle E
authors: KE
authors: Roberts
authors: Ivelin
authors: I
authors: Georgiev
authors: Ryan H
authors: RH
authors: Lilien
authors: Daniel A
authors: DA
authors: Keedy
authors: Cheng-Yu
authors: CY
authors: Chen
authors: Faisal
authors: F
authors: Reza
authors: Amy C
authors: AC
authors: Anderson
authors: David C
authors: DC
authors: Richardson
authors: Jane S
authors: JS
authors: Richardson
authors: Bruce R
authors: BR
authors: Donald
mesh_terms: D000465:Algorithms; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins