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OSPREY specifications

Information


Unique identifier OMICS_10812
Name OSPREY
Alternative names Open Source Protein REdesign for You, cOSPREY (cloud Open Source Protein REdesign for You)
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A protonated protein structure.
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Python
Parallelization CUDA
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Subtools


  • CATS
  • COMETS
  • DEEPer
  • Dynamic A*
  • EPIC
  • iMinDEE
  • K*
  • LUTE
  • PLUG
  • Protein:Protein Interactions

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline OSPREY
  • person_outline Bruce Donald
  • person_outline Mark Hallen

Additional information


The manual for the previous version can be consulted at: http://www.cs.duke.edu/donaldlab/software/osprey/osprey.2.2/OSPREY2.2.pdf The source code of the cloud version can be downloaded at: https://github.com/iiisthu/cOSPREY

Publications for Open Source Protein REdesign for You

OSPREY citations

 (9)
library_books

Path Planning for Non Circular, Non Holonomic Robots in Highly Cluttered Environments

2017
PMCID: 5579725
PMID: 28809785
DOI: 10.3390/s17081876

[…] e the calculation time. In addition, this algorithm provides a bound on the sub-optimality of the solution, which is the ϵ factor itself.When using replanning graph search algorithms, such as Anytime Dynamic A* (ADA*), a real-time convolution will be required for any newly found obstacles. This will also happen when using the technique based on the two inflated maps (inscribed and circunscribed). […]

library_books

A critical analysis of computational protein design with sparse residue interaction graphs

2017
PLoS Comput Biol
PMCID: 5391103
PMID: 28358804
DOI: 10.1371/journal.pcbi.1005346

[…] st if sparse residue interaction graphs could be a source of conformational difference between the predicted and experimentally observed residue conformations, we performed side-chain placement using osprey on the designed mutant of human procarboxypeptidase A2 (PDB id: 1VJQ). The structure of the designed mutant was used as input to rule out backbone changes as an additional source of error. We a […]

library_books

An Improved Simulated Annealing Technique for Enhanced Mobility in Smart Cities

2016
PMCID: 4970063
PMID: 27376289
DOI: 10.3390/s16071013

[…] ation metrics in smart cities is also presented. However, this is done without any performance evaluation.In [], the authors evaluate four algorithms: static Dijkstra, static A*, dynamic Dijkstra and dynamic A*. The evaluated algorithms have been applied in three different test scenarios (city centre, suburban and rural). According to the performance evaluation, the authors recommend the A*-based […]

library_books

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

2016
PLoS Comput Biol
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] that unlike discrete rotamer assignments, work by Donald and colleagues pursues continuous rotamers and is able to reach lower-energy conformations []. This functionality is integrated in the popular OSPREY software []. It is expected that the design of a smoothed backbone-dependent rotamer library in [], which allows evaluating rotamer characteristics as smooth and continuous functions of the ϕ, […]

library_books

Drivers’ Visual Behavior Guided RRT Motion Planner for Autonomous On Road Driving

2016
PMCID: 4732135
PMID: 26784203
DOI: 10.3390/s16010102

[…] the robot is mapped to a set of grid cells, where each grid cell represents an existing obstacle at that grid position in the environment. The optimal path search methods, such as the A* and Anytime dynamic A* algorithms, are usually used to determine a globally optimal path that connects each grid cell from an initial position to a goal position while avoiding static and dynamic obstacles in the […]

library_books

Structure based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance

2015
PMCID: 4470366
PMID: 26151066
DOI: 10.1038/mtm.2015.21

[…] terial activity. Molecular mechanics energies (a proxy for stability and thereby maintenance of function) were computed according to AMBER as implemented under the open source protein design software OSPREY. For each stage and each mutational load from 2 to 8, the Pareto frontier designs were supplemented with designs comprising 19 successive near-optimal frontiers.Stage 2 lead variants were selec […]

Citations

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OSPREY institution(s)
Department of Computer Science, Duke University, Durham, NC, USA; Department of Chemistry, Duke University, Durham, NC, USA; Toyota Technological Institute at Chicago, Chicago, IL, USA; Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, NC, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
OSPREY funding source(s)
Supported by the NIH (grants R01 GM-78031 and R01 GM-118543), NSF (Graduate Research Fellowship), PhRMA Foundation (Informatics Predoctoral Fellowships), and the Liebmann Foundation (fellowship).

OSPREY review

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Promising alternative to Rosetta with a liberal license.