COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.

Nucleic Acids Research
Ambrish RoyYang Zhang

Abstract

We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein-ligand binding interactions, Enzyme Commission number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale benchmarking tests and demonstrated significant advantages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein-ligand binding site predictions. The COFACTOR sever and the template libraries are freely available at http://zhanglab.ccmb.med.umich.edu/COFACTOR.

References

Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 4, 2004·American Journal of Pharmacogenomics : Genomics-related Research in Drug Development and Clinical Practice·Helen M Berman, John D Westbrook
Nov 9, 2004·Bioinformatics·Johannes Söding
Dec 21, 2004·Nucleic Acids Research·S VelankarK Henrick
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Jun 21, 2005·Current Opinion in Structural Biology·James D WatsonJanet M Thornton
Jun 28, 2005·Nucleic Acids Research·Thomas YanSeung Y Rhee
Jun 17, 2006·BMC Bioinformatics·Andreas SchlickerThomas Lengauer
Mar 9, 2007·Bioinformatics·James Z WangChin-Fu Chen
May 24, 2007·Bioinformatics·John A Capra, Mona Singh
Jan 1, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michal Brylinski, Jeffrey Skolnick
Jul 5, 2008·Briefings in Functional Genomics & Proteomics·Pier Federico Gherardini, Manuela Helmer-Citterich
Oct 30, 2008·Nucleic Acids Research·Daniel BarrellRolf Apweiler
Mar 31, 2009·Current Opinion in Structural Biology·Yang Zhang
Jul 16, 2009·Proteins·Georgii G KrivovRoland L Dunbrack
Aug 4, 2009·PLoS Computational Biology·Catia PesquitaFrancisco M Couto
Dec 10, 2009·PLoS Computational Biology·John A CapraThomas A Funkhouser
Feb 19, 2010·Bioinformatics·Jinrui Xu, Yang Zhang
Oct 14, 2010·Proteins·Lidia Prieto, Themis Lazaridis
Jul 1, 2006·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Angel Herráez
Oct 12, 2011·Proteins·Tobias SchmidtTorsten Schwede

❮ Previous
Next ❯

Citations

Aug 7, 2013·Biochemical and Biophysical Research Communications·Abhishek KumarFrank Kempken
Dec 18, 2012·Journal of Chemical Information and Modeling·Hongyi Zhou, Jeffrey Skolnick
Sep 3, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Dong XuYang Zhang
Jun 14, 2013·Nucleic Acids Research·Daniel B RocheLiam J McGuffin
May 3, 2013·PeerJ·Derek J TaylorJeremy A Bruenn
Oct 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Shivas R AminOlivier Lichtarge
Nov 12, 2013·Journal of Theoretical Biology·Sweta KumariMohammad Tauqueer
May 8, 2014·Biochemical and Biophysical Research Communications·Sung Bae Kim, Hiroshi Izumi
Apr 10, 2014·Biochimica Et Biophysica Acta·Susana A L LoboLígia M Saraiva
Mar 25, 2014·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Qihai XiaoRongping Zhang
Apr 3, 2014·Developmental and Comparative Immunology·Nikolay V OgryzkoHeather L Wilson
Aug 12, 2014·Biochemistry. Biokhimii︠a︡·S S MakarovaS Y Morozov
Aug 29, 2014·TheScientificWorldJournal·Md Anowar Hossain, Hairul Azman Roslan
Jun 27, 2014·Developmental and Comparative Immunology·Na XuShicui Zhang
May 28, 2014·Nucleic Acids Research·Janez Konc, Dušanka Janežič
Aug 6, 2014·Journal of Biotechnology·Dawn Elizabeth StephensKugen Permaul
Dec 26, 2013·The Journal of Cell Biology·Michael J OphirStephen C Bunnell
Oct 18, 2013·Journal of Molecular Modeling·Xin ChenQi Wang
Sep 8, 2012·Journal of Structural and Functional Genomics·Alexander Zawaira, Youtaro Shibayama
Jan 17, 2016·Computational Biology and Chemistry·Leonardo D Garma, André H Juffer
Nov 6, 2015·International Journal of Molecular Sciences·Mayumi EgusaShinsuke Ifuku
Sep 12, 2013·Critical Reviews in Biotechnology·Vineet Kumar SrivastavaNarendra Tuteja
Jan 6, 2016·International Journal of Biological Macromolecules·Faez Iqbal KhanShams Tabrez
Jan 23, 2016·Frontiers in Molecular Neuroscience·Vera M KalscheuerRobert J Harvey
Nov 19, 2013·Nucleic Acids Research·Paolo MaiettaMichael L Tress
Jul 1, 2015·Proceedings of the National Academy of Sciences of the United States of America·Chen-Ching YuanDanuta Szczesna-Cordary
Feb 19, 2013·Current Opinion in Structural Biology·Jeffrey SkolnickMu Gao
Aug 27, 2015·Chemical Biology & Drug Design·Matthew Bartolowits, V Jo Davisson
Dec 24, 2015·International Journal of Molecular Sciences·Daniel Barry RocheLiam James McGuffin
Oct 3, 2015·Methods : a Companion to Methods in Enzymology·Woong-Hee ShinDaisuke Kihara

❮ Previous
Next ❯

Datasets Mentioned

BETA
GM084222

Software Mentioned

COFACTOR
PSI
TASSER
Scwrl4
ConCavity
HHsearch
FINDSITE
Jmol
TM
Catalytic Site Atlas

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.