SCOWLP classification: structural comparison and analysis of protein binding regions

BMC Bioinformatics
Joan TeyraM Teresa Pisabarro

Abstract

Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Protein binding regions (PBRs) might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classi...Continue Reading

References

Oct 27, 1998·Trends in Biochemical Sciences·K Henrick, J M Thornton
Oct 17, 2002·Protein Science : a Publication of the Protein Society·Angel R OrtizOsvaldo Olmea
Mar 27, 2004·Protein Science : a Publication of the Protein Society·Ozlem KeskinRuth Nussinov
Sep 24, 2004·Proteins·K GunasekaranRuth Nussinov
Dec 21, 2004·Nucleic Acids Research·Amelie SteinPatrick Aloy
Jan 20, 2005·Bioinformatics·Fred P Davis, Andrej Sali
Jun 9, 2005·Bioinformatics·Dmitry LupyanAngel R Ortiz
Jul 2, 2005·Nucleic Acids Research·Utkan OgmenAttila Gursoy
Oct 26, 2005·Proteins·Wan Kyu Kim, Jon C Ison
Dec 31, 2005·Nucleic Acids Research·Christof WinterMichael Schroeder
Jan 21, 2006·BMC Bioinformatics·Hongbo ZhuThomas Lengauer
Oct 3, 2006·PLoS Computational Biology·Wan Kyu KimMichael Schroeder

❮ Previous
Next ❯

Citations

Jan 9, 2013·Journal of Molecular Modeling·Jelena RandjelovićVladimir Savić
Nov 26, 2010·Journal of Computer-aided Molecular Design·Katarzyna PrymulaIrena Roterman
Feb 10, 2010·Omics : a Journal of Integrative Biology·Sanket P BorgaonkarMia K Markey
Feb 26, 2009·Briefings in Bioinformatics·Nurcan TuncbagRuth Nussinov
Nov 5, 2011·Nucleic Acids Research·Guilhem FaureRaphaël Guerois
Jun 30, 2009·Current Opinion in Pulmonary Medicine·Keattiyoat Wattanakit, Mary Cushman
Mar 10, 2010·Biochemistry. Biokhimii︠a︡·A A TerentievK V Shaitan
Apr 17, 2009·BMC Structural Biology·Sergey A SamsonovM Teresa Pisabarro
May 27, 2010·PLoS Computational Biology·Amelie Stein, Patrick Aloy
Nov 26, 2013·Nucleic Acids Research·Anisah W GhoorahDavid W Ritchie
Feb 16, 2011·Current Opinion in Structural Biology·Amelie SteinPatrick Aloy
Oct 15, 2013·Proteins·Anisah W GhoorahDavid W Ritchie
Mar 24, 2016·Environmental Science & Technology·Yinon MazarYinon Rudich
Apr 14, 2016·Chemical Reviews·Ozlem KeskinAttila Gursoy
Jul 19, 2013·Journal of the American Chemical Society·Mikhail O Maksimov, A James Link
Jul 12, 2017·Journal of the American Chemical Society·Chuhan ZongA James Link
Nov 16, 2011·Evolutionary Bioinformatics Online·Bo ZhuRené De Mot
Aug 24, 2010·Journal of Chemical Information and Modeling·Peng ZhouZhicai Shang

❮ Previous
Next ❯

Software Mentioned

PRISM
SCOWLP
MAMMOTH
MySQL
Jmol
Java

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.