KVFinder protocols

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KVFinder specifications

Information


Unique identifier OMICS_04688
Name KVFinder
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C, C++, Python
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Requirements
PyMOL
Maintained Yes

Versioning


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Maintainer


  • person_outline Paulo SL de Oliveira <>

Publication for KVFinder

KVFinder in pipeline

2016
PMCID: 5347970
PMID: 28033660
DOI: 10.1002/bdrc.21145

[…] its corresponding mutated molecules. the final confirmation of the lowest energy models was confirmed for each pair of simulations. the volumes of the cavities of the models were calculated using kvfinder (oliveira et al., ). molecular models were drawn using pymol (www.pymol.org)., transient gene expression assays were performed using human embryonic kidney tsa‐201 cells to analyze […]


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KVFinder in publications

 (8)
PMCID: 5630584
PMID: 28986565
DOI: 10.1038/s41598-017-13155-z

[…] dopamine-gαi-bound simulation is defined to start from 1 μs. , *since the gαi subunit is bound to the 1.0 μs d3r, the dopamine-gαi-bound simulation is defined to start from 1 μs., the pymol plugin kvfinder, is a tool for cavity prospection and spatial characterization. this tool uses a geometrical grid-based method, in which a target protein is inserted into a 3d grid. points within this grid […]

PMCID: 5587760
PMID: 28878230
DOI: 10.1038/s41598-017-10932-8

[…] amino acid position conservation displayed by the consurf server were projected onto the mesoamp structure. the molecular docking was calculated using m-zdock. the cavity volumes were calculated by kvfinder, and the pymol software was used to visualize the models and to prepare the figures., preparation of plasmids, dna manipulations, and transformation of e. coli bl21(de3) competent cells […]

PMCID: 5572447
PMID: 28902287
DOI: 10.1590/0074-02760160522

[…] 3v server () to explore structural features of the active site (volume, surface area, sphericity, and effective radius). the characterization of the active site binding cavities was performed with kvfinder using default parameters (., grouping leishmanolysins according to their insertion regions reveals three distinct subgroups - from the multiple sequence alignment of the 29 leishmanolysin […]

PMCID: 5531557
PMID: 28750094
DOI: 10.1371/journal.pone.0182043

[…] 0.8.2 [], and pymol 1.7 (www.pymol.org) []. topology diagram of the secondary structures of lra-12 was performed with pdbsum []. prediction of cavities within the β-lactamase was performed with kvfinder plugin for pymol []., the coordinates and structure factors of the native lra-12 β-lactamase were deposited under accession code 5aeb (released: 2015-09-16)., the predicted amino acid […]

PMCID: 5517649
PMID: 28724971
DOI: 10.1038/s41598-017-06332-7

[…] three-fold symmetry prevents internal residues of mitsuba-1 from approaching the symmetry axis too closely, and a central cavity is found in the structure with a volume close to 100 å3 according to kvfinder. mytilec-1 has a smaller cavity with a volume of about 40 å3.table 1values in parentheses are for the highest resolution shell. br factor is ∑h||fo(h)| − |fc(h)||/∑h fo(h), where fo and fc […]


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KVFinder institution(s)
National Laboratory of Biosciences, Campinas, SP, Brazil
KVFinder funding source(s)
This work was supported by grants from São Paulo Research Foundation (2009/06433-0 and 2008-52695-4) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior.

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