CODA: a combined algorithm for predicting the structurally variable regions of protein models.

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filt...

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Main Authors: Deane, C, Blundell, T
Format: Journal article
Language:English
Published: 2001
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author Deane, C
Blundell, T
author_facet Deane, C
Blundell, T
author_sort Deane, C
collection OXFORD
description CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.
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spelling oxford-uuid:7a935729-dce4-4362-b768-e8bd8c5a5d2e2022-03-26T20:44:53ZCODA: a combined algorithm for predicting the structurally variable regions of protein models.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:7a935729-dce4-4362-b768-e8bd8c5a5d2eEnglishSymplectic Elements at Oxford2001Deane, CBlundell, TCODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.
spellingShingle Deane, C
Blundell, T
CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title_full CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title_fullStr CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title_full_unstemmed CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title_short CODA: a combined algorithm for predicting the structurally variable regions of protein models.
title_sort coda a combined algorithm for predicting the structurally variable regions of protein models
work_keys_str_mv AT deanec codaacombinedalgorithmforpredictingthestructurallyvariableregionsofproteinmodels
AT blundellt codaacombinedalgorithmforpredictingthestructurallyvariableregionsofproteinmodels