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Calcium Model 2015
The FEATURE calcium model was trained on a total of 314 calcium sites and 2,735 non-sites from 312 protein structures taken from the RCSB Protein Data Bank (PDB) using FEATURE 3.1. The calcium model provides the FEATURE scores for given points in a crystal structure, where higher scores indicate a higher likelihood of being an actual calcium site.
Calcium Model releases
Jul 21, 2015

Calcium 2015 distribution files.

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Jul 21, 2015
14 MB
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Data/images/video
Calcium 2015 distribution tarball prepared by Weizhuang Zhou


Errata to PLOS Publication
Errata to PLOS Publication (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091240)
Final results 2017
May 24, 2017

Final results of homology filter bug investigation

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May 24, 2017
631 MB
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Data/images/video


FEATURE 1.9 with Calcium Model
FEATURE 1.9.1 stable release archive; if you are new to FEATURE, download FEATURE 3.0 instead.
Archive: FEATURE 1.9.1 and 2007 Calcium Binding Model
Jul 30, 2012

This release is for users who need the Ca++ binding model; new FEATURE users should download and use FEATURE 3.0 instead. Click the links below to download the FEATURE 1.9 source code for UNIX, Linux, Mac OS X, Windows/CYGWIN systems. This package also includes Ca++ binding model ca.model, originally released in 2007.

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Jul 30, 2012
315 KB
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Source code
FEATURE 1.9.1 source code and Ca++ model


FEATURE 3.1
FEATURE 3.1 Stable Release
Release Build 1636
Jan 24, 2014

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Apr 22, 2014
39 MB
Any
Source code
feature-3.1.0-src.tar.gz

Documentation Links

Feb 18, 2014
FEATURE User Manual


FEATURE Models
Contains the SeqFEATURE library of models consisting of 136 models derived from 53 PROSITE patterns, plus an aditional 4 earlier manually curated models. All models were developed by the Stanford FEATURE development team
model files
Jun 18, 2010

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Nov 11, 2015
5 MB
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Data/images/video
606 FEATURE models released 2013 using SeqFEATURE method

Jun 17, 2010
866 KB
Any
Source code
models developed by the Stanford FEATURE development team; contains 2 directories of models. Please also see README files below.

Documentation Links

Jun 21, 2010
References and additional information for the 136 SeqFeature Models

Jun 21, 2010
References and additional information for ATP, Calcium, Chloride and Mg Models

PLEASE CITE THESE PAPERS

[FEATURE Framework] ********** "The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications." Halperin I, Glazer DS, Wu S, Altman RB. BMC Genomics. 9 Suppl 2 S2. (2008) View

[SeqFEATURE Models] ********** "The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation." Wu S, Liang MP, Altman RB. Genome Biol. 9 (1): R8. (2008) View

[RNA_DiffBndMg & RNA_SiteBndMg Models] ********** "Microenvironment analysis and identification of magnesium binding sites in RNA." Banatao DR, Altman RB, Klein TE. Nucleic Acids Res. 31(15): 4450-60. (2003) View

[ATP, Calcium & Chloride Models] ********** "Recognizing protein binding sites using statistical descriptions of their 3D environments." Wei L, Altman RB. Pac Symp Biocomput. 497-508. (1998) View


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