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

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Publication for FINDSITE-metal

FINDSITE-metal in publications

 (4)
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 [], […]

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

[…] 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 […]

PMCID: 3686302
PMID: 23802014
DOI: 10.3389/fgene.2013.00118

[…] 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 […]

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

[…] 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 […]


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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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