KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

Nucleic Acids Research
João P G L M RodriguesGaurav Chopra

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 ...Continue Reading

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Citations

Jun 6, 2013·Nucleic Acids Research·Lim HeoChaok Seok
Oct 5, 2013·The Journal of Chemical Physics·A DasS S Plotkin
Dec 22, 2015·Journal of Structural Biology·Nicolás González BardeciSilvia Moreno
Aug 1, 2013·Proteins·Timothy NugentDavid T Jones
Mar 29, 2014·Proteins·George A KhourySilvia N Crivelli
Aug 6, 2013·Proteins·J P G L M RodriguesAlexandre M J J Bonvin
Apr 29, 2016·Biochemistry Research International·B SenthilkumarR Rajasekaran
Sep 10, 2015·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Vivek K VyasSurmil Shah
Aug 9, 2015·Interdisciplinary Sciences, Computational Life Sciences·Manoj Kumar Yadav, D Swati
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Feb 12, 2014·Journal of Theoretical Biology·Navid NezafatEskandar Omidinia
Jan 18, 2015·Chemico-biological Interactions·Vivek K VyasPalak Patel
May 1, 2016·Nucleic Acids Research·Debswapna BhattacharyaJianlin Cheng
Jun 23, 2016·Chemical Reviews·Sebastian KmiecikAndrzej Kolinski
Jul 16, 2016·PloS One·Bruna Baumgarten Krebs, Joelma Freire De Mesquita
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Dec 6, 2018·Genes·Eshel FaraggiAndrzej Kloczkowski
May 10, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gideon K GogoviEstela Blaisten-Barojas
May 12, 2019·International Journal of Molecular Sciences·Recep Adiyaman, Liam James McGuffin
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Jun 18, 2017·Cell Death and Differentiation·Udaya K Tiruttani SubhramanyamJoerg Labahn

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Software Mentioned

Linux
jQuery
KoBaMIN
Biopython
DataTables
KnowMIN
MESHI
ENCAD
Jmol
HA

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