The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
Open accessAbstract
Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site. Contact: pyrosetta@graylab.jhu.edu
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Cites
The PyMOL Molecular Graphics System
DeLano, W. L. (2002) · Medical Entomology and Zoology · Cited by 18,147
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Protein structure prediction and analysis using the Robetta server
Kim, D. E., Chivian, D., & Baker, D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh468 · Cited by 2,111
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., & Baker, D. (2003) · Science · doi:10.1126/science.1089427 · Cited by 1,670
Toward High-Resolution de Novo Structure Prediction for Small Proteins
Bradley, P., Misura, K. M. S., & Baker, D. (2005) · Science · doi:10.1126/science.1113801 · Cited by 864
Native protein sequences are close to optimal for their structures
Kuhlman, B., & Baker, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.19.10383 · Cited by 810
A simple physical model for binding energy hot spots in protein–protein complexes
Kortemme, T., & Baker, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202485799 · Cited by 804
The RosettaDock server for local protein-protein docking
Lyskov, S., & Gray, J. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn216 · Cited by 592
Self-citationStructure prediction for CASP8 with all‐atom refinement using Rosetta
Raman, S., Vernon, R., Thompson, J., Tyka, M., Sadreyev, R., Pei, J., Kim, D., Kellogg, E., DiMaio, F., Lange, O., et al. (2009) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22540 · Cited by 518
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00125 · Cited by 1,532
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Metadata
- Authors
- Chaudhury, S., Lyskov, S., & Gray, J. J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-01-07
- Volume
- 26
- Issue
- 5
- Pages
- 689-691
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2151581834
- Cited by
- 816
- References
- 15
- FWCI
- 5.08
- Type
- journal article
- Language
- en
- Open access
- bronze
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