BindML specifications

Information


Unique identifier OMICS_13707
Name BindML
Interface Web user interface
Restrictions to use None
Input data Email, PDB File, PDB Chain ID, Multiple Sequence Alignment File
Input format PDB, FASTA
Output data The interactive BindML output consists of an integrative structural-level view and a residue-level view with associated prediction scores.
Output format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Daisuke Kihara <>

Additional information


An old version is available on http://kiharalab.org/bindml/

Information


Unique identifier OMICS_13707
Name BindML
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Email, PDB File, PDB Chain ID, Multiple Sequence Alignment File
Input format PDB, FASTA
Output data The interactive BindML output consists of an integrative structural-level view and a residue-level view with associated prediction scores.
Output format PDB
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Daisuke Kihara <>

Additional information


An old version is available on http://kiharalab.org/bindml/

Publications for BindML

BindML in publication

PMCID: 4338852
PMID: 25713596
DOI: 10.1186/s13015-015-0033-9

[…] off the evolutionary trace approach [-], constructing phylogenetic distance trees to extract a residue ranking based on evolutionary importance, then using this to derive likely ppiss. similarly, bindml [] uses local msas, specialized substitution matrices, and phylogenetic tree construction to obtain the likelihood that a given patch msa belongs to a ppis (described below). homppi [] derives […]


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BindML institution(s)
Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN, USA; Department of Computer Science, College of Science, Purdue University, West Lafayette, IN, USA; Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
BindML funding source(s)
This work was supported in part by the National Institute of General Medical Sciences of the National Institutes of Health (R01 GM075004) and the National Science Foundation (DMS800568, IIS0915801, EF0850009).

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