KVFinder statistics

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Citations per year

Number of citations per year for the bioinformatics software tool KVFinder
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Tool usage distribution map

This map represents all the scientific publications referring to KVFinder per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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


No version available

Maintainer


  • person_outline Paulo SL de Oliveira

Publication for KVFinder

KVFinder citations

 (9)
library_books

Halotolerant aminopeptidase M29 from Mesorhizobium SEMIA 3007 with biotechnological potential and its impact on biofilm synthesis

2017
Sci Rep
PMCID: 5587760
PMID: 28878230
DOI: 10.1038/s41598-017-10932-8

[…] e 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. […]

call_split

Structural insights into leishmanolysins encoded on chromosome 10 of Leishmania (Viannia) braziliensis

2017
PMCID: 5572447
PMID: 28902287
DOI: 10.1590/0074-02760160522
call_split See protocol

[…] he 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 (. […]

library_books

Computational design of a symmetrical β trefoil lectin with cancer cell binding activity

2017
Sci Rep
PMCID: 5517649
PMID: 28724971
DOI: 10.1038/s41598-017-06332-7

[…] e 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. Figure 2 Figure 3 A direct comparison of the Mitsuba-1 structure with the entire PDB was carried out with DALI. Unsurprisingly, t […]

library_books

Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals

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

[…] and 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). […]

library_books

Bg10: A Novel Metagenomics Alcohol Tolerant and Glucose Stimulated GH1 ß Glucosidase Suitable for Lactose Free Milk Preparation

2016
PLoS One
PMCID: 5176175
PMID: 28002476
DOI: 10.1371/journal.pone.0167932

[…] nity is most evident []. Similarly, depicts the same view shown in , providing evidence of the shape and importance of the active pocket present in Bg10, according to the prediction generated by the KVFinder plugin installed in the PyMOL software. Thus, these results for Bg10 agree with the evidence provided by Giuseppe and co-workers [], which indicates that this enzyme is also tolerant/stimulat […]

call_split

Evaluation of a novel virtual screening strategy using receptor decoy binding sites

2016
PMCID: 4994241
PMID: 27553084
DOI: 10.1186/s12952-016-0058-8
call_split See protocol

[…] all actives),Ndecoys = the total number of inactive decoys,Ninactives = the number of decoys chosen at x% of the ligand/decoy database.Binding site and decoy sites were analysed post-docking with the KVFinder Cavity Detection PyMol Plugin [] to provide a quantitative description of the two sites. The software enables comparison and characterisation of protein binding sites by the number, area and […]


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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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