High-throughput identification of interacting protein-protein binding sites.

High-throughput identification of interacting protein-protein binding sites. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

High-throughput identification of interacting protein-protein binding sites. Abstract Text:

Jo-Lan Chung,Wei Wang,Philip E Bourne,

BACKGROUND: With the advent of increasing sequence and structural data, a number of methods have been proposed to locate putative protein binding sites from protein surfaces. Therefore, methods that are able to identify whether these binding sites interact are needed. RESULTS: We have developed a new method using a machine learning approach to detect if protein binding sites, once identified, interact with each other. The method exploits information relating to sequence and structural complementary across protein interfaces and has been tested on a non-redundant data set consisting of 584 homo-dimers and 198 hetero-dimers extracted from the PDB. Results indicate 87.4% of the interacting binding sites and 68.6% non-interacting binding sites were correctly identified. Furthermore, we built a pipeline that links this method to a modified version of our previously developed method that predicts the location of binding sites. CONCLUSION: We have demonstrated that this high-throughput pipeline is capable of identifying binding sites for proteins, their interacting binding sites and, ultimately, their binding partners on a large scale.

High-throughput identification of interacting protein-protein binding sites. Publishing Authors By Initials

JL Chung,W Wang,PE Bourne,

For similar investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research abstracts see: investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research

PUBMED ID PMID:

MEDLINE DATE:

High-throughput identification of interacting protein-protein binding sites. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: BMC bioinformatics

VOLUME: 8

Page Numbers: 223

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 27

MONTH: 06

YEAR: 2007

High-throughput identification of interacting protein-protein binding sites. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965194

High-throughput identification of interacting protein-protein binding sites. Keywords Mesh Terms:

KEYWORDS: Sequence Analysis, Protein

MESH TERMS: methods

Chemical & Substance for Abstract: High-throughput identification of interacting protein-protein binding sites. Information

Substance Name: Amino Acids

Registry Number: 0

Grant and Affiliation Information for High-throughput identification of interacting protein-protein binding sites.

AFFILIATION: Department of Pharmacology, University of California, San Diego, Gilman Drive, La Jolla, CA 92093-0743, USA.

Country: England

AGENCY: United States NIGMS

GRANT: GM63208

ACRONYM: GM

MEDLINETA: BMC Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

High-throughput identification of interacting protein-protein binding sites Related Publications

• A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
• Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.
• Bound attractant at the leading vs. the trailing edge determines chemotactic prowess.
• Changes in corneal thickness in patients with treated and untreated ocular hypertension.
• Con-Struct Map: a comparative contact map analysis tool.
• Effects of glaucoma medications on corneal endothelium, keratocytes, and subbasal nerves among participants in the ocular hypertension treatment study.
• Femtosecond laser versus mechanical microkeratome for LASIK: a randomized controlled study.
• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.
• High-throughput identification of interacting protein-protein binding sites.
• Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2.
• Linking children's neuropsychological processing of emotion with their knowledge of emotion expression regulation.
• Measuring corneal thickness with the ConfoScan 4 and z-ring adapter.
• Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry.
• Nutrition and HIV/AIDS in infants and children in South Africa: implications for food-based dietary guidelines.
• OC48: Development of a model to predict ability of ultrasound to make a diagnosis at first assessment in the unselected early pregnancy population.
• OC58: Ectopic pregnancy diagnosis and management: a 4-year experience.
• OC59: A single transvaginal ultrasound examination as a test for ectopic pregnancy.
• OC63: Why are some ectopic pregnancies missed on the initial ultrasound examination?
• OC64: Pain does not predict ultrasound diagnosis of ectopic pregnancy in the Early Pregnancy Unit.
• OC65: Anechoic free peritoneal fluid in early intrauterine pregnancy.
• OC67: Persisting pregnancies of unknown location: challenges in diagnosis and management.
• OP04.01: Has ultrasound eliminated the need for a vaginal speculum examination in the assessment of women with bleeding in early pregnancy?
• OP17.03: The impact of a two-week referral rapid access ultrasound-based clinic to assess women considered at high-risk of gynecological malignancy.
• Objective measurement of backscattered light from the anterior and posterior cornea in vivo.
• Polarity reveals intrinsic cell chirality.
• Prediction of ectopic pregnancy in women with a pregnancy of unknown location.
• Rac and Cdc42 play distinct roles in regulating PI(3,4,5)P3 and polarity during neutrophil chemotaxis.
• South African paediatric food-based dietary guidelines.
• Structural evolution of the protein kinase-like superfamily.
• The optic nerve head in glaucoma.