FINDSITE-metal statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FINDSITE-metal
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Tool usage distribution map

This map represents all the scientific publications referring to FINDSITE-metal per scientific context
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FINDSITE-metal specifications

Information


Unique identifier OMICS_25462
Name FINDSITE-metal
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format PDB
Computer skills Basic
Stability Stable
Source code URL http://cssb.biology.gatech.edu/skolnick/files/LHM/FINDSITE-metal/findsitemetal-1.0.tar.gz
Maintained No

Documentation


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This tool is not available anymore.

Publication for FINDSITE-metal

FINDSITE-metal citations

 (4)
library_books

Computational approaches for de novo design and redesign of metal binding sites on proteins

2017
Biosci Rep
PMCID: 5482196
PMID: 28167677
DOI: 10.1042/BSR20160179

[…] the other hand, MetalPredator [] utilizes two libraries of Hidden Markov Model profiles representative of Pfam domains and structural motifs that bind Fe/S clusters. Some prediction software such as FINDSITE-metal [], mFASD [], TEMSP [], FEATURE metal scanning [–] utilize structural information for prediction of the metal ion-binding sites. A few of them such as MetSite [], 3DLigandSite [], Fragm […]

library_books

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014
Adv Bioinformatics
PMCID: 3977119
PMID: 24778647
DOI: 10.1155/2014/501841

[…] r preference to bind Mn2+ than glutamic acid and histidine.Information on amino acid preferences and geometry of coordination spheres is used in algorithms for metal binding sites prediction, such as FINDSITE-metal [], MetalDetector v2.0 [], Fold-X [], and FlexX []. However, the information on preferable 3D structural motifs is available mostly for Ca2+ and Zn2+ binding proteins. Well-known EF-han […]

library_books

Unleashing the power of meta threading for evolution/structure based function inference of proteins

2013
Front Genet
PMCID: 3686302
PMID: 23802014
DOI: 10.3389/fgene.2013.00118

[…] ly structurally similar to the target. Similar criteria are commonly used for the template identification in protein function prediction. For example, to collect functional templates, FINDSITE () and FINDSITE-metal () use a threading Z-score of ≥4, a threshold that is also used in the detection of structural templates in TASSER (). A similar method, @TOME-2, employs meta-threading to detect templa […]

library_books

Candida albicans Scavenges Host Zinc via Pra1 during Endothelial Invasion

2012
PLoS Pathog
PMCID: 3386192
PMID: 22761575
DOI: 10.1371/journal.ppat.1002777

[…] the predicted structures. The Pra1 best structural hit (Deuterolysin from A. oryzae) was additionally identified using SWISS-MODEL tool (swissmodel.expasy.org) and metal binding sites predicted with Findsite-metal (cssb.biology.gatech.edu/findsite-metal) and 3D ligand site (www.sbg.bio.ic.ac.uk/3dligandsite). To predict interactions between the two proteins, the structures generated in Phyre2 we […]


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FINDSITE-metal institution(s)
Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA, USA
FINDSITE-metal funding source(s)
Supported by grant No. GM-48835 and GM-37408 of the Division of General Medical Sciences of the National Institutes of Health.

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