Rappertk: a versatile engine for discrete restraint-based conformational sampling of macromolecules
BMC STRUCTURAL BIOLOGY
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Gore, S., Karmali, A., & Blundell, T. (2007). Rappertk: a versatile engine for discrete restraint-based conformational sampling of macromolecules. BMC STRUCTURAL BIOLOGY, 7 https://doi.org/10.1186/1472-6807-7-13
Background: Macromolecular structures are modeled by conformational optimization within experimental and knowledge-based restraints. Discrete restraint-based sampling generates high-quality structures within these restraints and facilitates further refinement in a continuous all-atom energy landscape. This approach has been used successfully for protein loop modeling, comparative modeling and electron density fitting in X-ray crystallography.|Results: Here we present a software toolkit (Rappertk) which generalizes discrete restraint-based sampling for use in structural biology. Modular design and multi-layered architecture enables Rappertk to sample conformations of any macromolecule at many levels of detail and within a variety of experimental restraints. Performance against a C-alpha-tracing benchmark shows that the efficiency has not suffered despite the overhead required by this flexibility. We demonstrate the toolkit's capabilities by building high-quality beta-sheets and by introducing restraint-driven sampling. RNA sampling is demonstrated by rebuilding a protein-RNA interface. Ability to construct arbitrary ligands is used in sampling protein- ligand interfaces within electron density. Finally, secondary structure and shape information derived from EM are combined to generate multiple conformations of a protein consistent with the observed density.|Conclusion: Through its modular design and ease of use, Rappertk enables exploration of a wide variety of interesting avenues in structural biology. This toolkit, with illustrative examples, is freely available to academic users from http://www-cryst.bioc.cam.ac.uk/similar to swanand/mysite/rtk/index.html.
simulation, PREDICTION, REFINEMENT, PROTEIN STRUCTURES, AB-INITIO CONSTRUCTION, POLYPEPTIDE FRAGMENTS, BACKBONE, FORCE-FIELD, LIBRARY
External DOI: https://doi.org/10.1186/1472-6807-7-13
This record's URL: http://www.dspace.cam.ac.uk/handle/1810/238040
Rights Holder: Gore et al.; licensee BioMed Central Ltd.