Software Developed by the Donald Lab
OSPREY
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Welcome to the website for the OSPREY (Open Source Protein REdesign for You) software. Here, you can download the newest version of the software, read the user manual and license agreement, or e-mail inquiries. You can also view a brief OSPREY slideshow tutorial.
OSPREY is a suite of programs for computational structure-based protein design. OSPREY is developed in the lab of Prof. Bruce Donald at Duke University. Citations to the primary papers for our work can be found here.
OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule inhibitors. With certain limitations, the current version of OSPREY can also model protein-protein and protein-peptide interactions.
OSPREY incorporates several different algorithmic modules for structure-based protein design, including a number of powerful Dead-End Elimination algorithms and the ensemble-based K* algorithm for protein-ligand binding prediction. OSPREY allows the incorporation of continuous protein side-chain and continuous or discrete backbone flexibility, while maintaining provable guarantees with respect to the input model (input structure, rotamer library, and energy function) for a given protein design problem. See full details of the different algorithmic modules in OSPREY.
To our knowledge, OSPREY is the only open-source, freely-available implementation of the DEE/A* algorithms. DEE/A* combines the provable Dead-End Elimination (DEE) algorithms with the A* search enumeration. OSPREY also includes many extensions and improvements to the DEE framework (e.g., minDEE, K*, DACS, BD, BRDEE). These extensions improve efficiency and allow the modelling of molecular flexibility. OSPREY includes the K* (pronounced "K-star") module, which is a provably-good ε-approximation (epsilon-approximation) algorithm for computing binding constants (KD) over molecular ensembles of the bound and unbound states of a protein:ligand complex using minimized DEE/A* (namely, minDEE/A*/K*). See the OSPREY manual and our papers for details. A shorter list of the primary papers underlying our software can be found here.
OSPREY is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (optionally) any later version. OSPREY is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Full licensing details, including citation requirements for the various different modules of the software, are found here.