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

Protein Science : a Publication of the Protein Society
C M Deane, T L Blundell

Abstract

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 modeli...Continue Reading

References

Mar 1, 1992·Protein Science : a Publication of the Protein Society·U HobohmC Sander
Feb 1, 1992·Protein Science : a Publication of the Protein Society·J OveringtonT L Blundell
Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Apr 1, 1992·Proteins·A L MorrisJ M Thornton
Dec 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·A C MartinA R Rees
Aug 20, 1987·Journal of Molecular Biology·C Chothia, A M Lesk
Jul 11, 1985·Nature·B L Sibanda, J M Thornton
Jun 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·J Greer
Jul 1, 1995·Nature Structural Biology·M B SwindellsJ M Thornton
Jul 1, 1995·Protein Science : a Publication of the Protein Society·S SudarsanamS Srinivasan
Mar 1, 1994·Protein Science : a Publication of the Protein Society·U Hobohm, C Sander
Jan 1, 1994·Critical Reviews in Biochemistry and Molecular Biology·M S JohnsonT L Blundell
Feb 1, 1994·Protein Engineering·G ChelvanayagamP Argos
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Sep 1, 1993·Protein Science : a Publication of the Protein Society·V ColluraJ Garnier
Apr 1, 1997·Current Opinion in Structural Biology·R Sánchez, A Sali
Mar 7, 1997·Journal of Molecular Biology·B OlivaM J Sternberg
Apr 11, 1997·Journal of Molecular Biology·H W van Vlijmen, M Karplus
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jan 1, 1997·Proteins·A C MartinJ M Thornton
Jun 27, 1998·Journal of Molecular Biology·U ReimerG Fischer
Nov 25, 1998·Protein Science : a Publication of the Protein Society·K MizuguchiJ P Overington
Aug 19, 1999·Proteins·U Lessel, D Schomburg
Oct 20, 1999·Proteins·T Alwyn Jones, G J Kleywegt
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne

❮ Previous
Next ❯

Citations

Oct 26, 2005·Journal of Molecular Modeling·Haiyan Jiang, Christian Blouin
Oct 27, 2005·Journal of Molecular Modeling·Neil J Harrison, Sarah C R Lummis
Dec 25, 2010·Journal of Computer-aided Molecular Design·Sébastien Dilly, Jean-François Liégeois
Feb 23, 2012·The Journal of Physical Chemistry. B·A Subramani, C A Floudas
Mar 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Daniel HoltbyMing Li
Jan 15, 2005·Thyroid : Official Journal of the American Thyroid Association·Ricardo Núñez MiguelJadwiga Furmaniak
Jun 8, 2010·Bioinformatics·Braddon K LanceGraham R Wood
Jun 28, 2005·Nucleic Acids Research·C AllandP Tufféry
Jul 18, 2006·Nucleic Acids Research·Narcis Fernandez-FuentesAndrás Fiser
Apr 18, 2006·Nucleic Acids Research·Narcis Fernandez-FuentesAndrás Fiser
May 4, 2013·Nucleic Acids Research·Jean-Paul EbejerCharlotte M Deane
Oct 30, 2008·Protein Engineering, Design & Selection : PEDS·Meng CuiRoman Osman
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom L BlundellDavid Burke
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Yanshun LiuDavid Eisenberg
May 29, 2004·Pharmacogenomics·Jurgen Kopp, Torsten Schwede
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Zhexin XiangBarry Honig
Jun 22, 2005·Expert Review of Proteomics·András Fiser
Dec 14, 2011·Advanced Drug Delivery Reviews·Tim WernerW Bret Church
Jun 5, 2003·Proteins·Manoj Pal, Swagata Dasgupta
Oct 14, 2005·Proteins·M Mönnigmann, C A Floudas
Feb 27, 2008·Proteins·Benjamin D SellersMatthew P Jacobson
Mar 26, 2008·Proteins·Michael A DolanDavid S Baker
Apr 11, 2012·Proteins·Jean-François St-Pierre, Normand Mousseau
Jul 6, 2010·Proteins·Benjamin D SellersMatthew P Jacobson
Aug 8, 2015·MAbs·Yoonjoo ChoiChris Bailey-Kellogg
Nov 19, 2011·Protein Science : a Publication of the Protein Society·Aashish N AdhikariTobin R Sosnick
Aug 10, 2006·Journal of Clinical Epidemiology·Cornelia H M van den EndeJoost Dekker
Feb 14, 2006·Journal of Molecular Biology·Vanita D Sood, David Baker
Aug 8, 2015·Bioinformatics·Mario Abdel MessihAnna Tramontano
Jan 1, 2013·Computational and Structural Biotechnology Journal·Yaohang Li
Apr 24, 2016·Nucleic Acids Research·Jochen IsmerPeter W Hildebrand
Feb 13, 2016·Mathematical Biosciences·Jun MengYu-Shi Luan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.