KoBaMIN: a knowledge-based minimization web server for protein structure refinement
Open Access
- 7 May 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (W1), W323-W328
- https://doi.org/10.1093/nar/gks376
Abstract
The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.Keywords
This publication has 16 references indexed in Scilit:
- Assessment of protein structure refinement in CASP9Proteins: Structure, Function, and Bioinformatics, 2011
- Consistent refinement of submitted models at CASP using a knowledge‐based potentialProteins, 2010
- Nature of the protein universeProceedings of the National Academy of Sciences of the United States of America, 2009
- Biopython: freely available Python tools for computational molecular biology and bioinformaticsBioinformatics, 2009
- Assessment of the protein‐structure refinement category in CASP8Proteins: Structure, Function, and Bioinformatics, 2009
- Solvent dramatically affects protein structure refinementProceedings of the National Academy of Sciences of the United States of America, 2008
- Progress and challenges in protein structure predictionCurrent Opinion in Structural Biology, 2008
- Near-native structure refinement using in vacuo energy minimizationProceedings of the National Academy of Sciences of the United States of America, 2007
- Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solutionComputer Physics Communications, 1995
- Refinement of protein conformations using a macromolecular energy minimization procedureJournal of Molecular Biology, 1969