Comparison of protein active site structures for functional annotation of proteins and drug design

Robert Powers, Jennifer C. Copeland, Katherine Germer, Kelly A. Mercier, Viswanathan Ramanatlian, Peter Revesz

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

Original languageEnglish (US)
Pages (from-to)124-135
Number of pages12
JournalProteins: Structure, Function and Genetics
Volume65
Issue number1
DOIs
StatePublished - Oct 1 2006

Fingerprint

Molecular Sequence Annotation
Drug Design
Catalytic Domain
Pharmaceutical Preparations
Proteins
Ligands
Databases
Drug Discovery
Software
Genes
Binding Sites
Genome

Keywords

  • CPASS
  • Functional annotation
  • Hypothetical proteins
  • Ligand-defined active sites

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

Comparison of protein active site structures for functional annotation of proteins and drug design. / Powers, Robert; Copeland, Jennifer C.; Germer, Katherine; Mercier, Kelly A.; Ramanatlian, Viswanathan; Revesz, Peter.

In: Proteins: Structure, Function and Genetics, Vol. 65, No. 1, 01.10.2006, p. 124-135.

Research output: Contribution to journalArticle

Powers, Robert ; Copeland, Jennifer C. ; Germer, Katherine ; Mercier, Kelly A. ; Ramanatlian, Viswanathan ; Revesz, Peter. / Comparison of protein active site structures for functional annotation of proteins and drug design. In: Proteins: Structure, Function and Genetics. 2006 ; Vol. 65, No. 1. pp. 124-135.
@article{b62c84600cf24b0cbe5ba9742ec95d63,
title = "Comparison of protein active site structures for functional annotation of proteins and drug design",
abstract = "Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.",
keywords = "CPASS, Functional annotation, Hypothetical proteins, Ligand-defined active sites",
author = "Robert Powers and Copeland, {Jennifer C.} and Katherine Germer and Mercier, {Kelly A.} and Viswanathan Ramanatlian and Peter Revesz",
year = "2006",
month = "10",
day = "1",
doi = "10.1002/prot.21092",
language = "English (US)",
volume = "65",
pages = "124--135",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "1",

}

TY - JOUR

T1 - Comparison of protein active site structures for functional annotation of proteins and drug design

AU - Powers, Robert

AU - Copeland, Jennifer C.

AU - Germer, Katherine

AU - Mercier, Kelly A.

AU - Ramanatlian, Viswanathan

AU - Revesz, Peter

PY - 2006/10/1

Y1 - 2006/10/1

N2 - Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

AB - Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

KW - CPASS

KW - Functional annotation

KW - Hypothetical proteins

KW - Ligand-defined active sites

UR - http://www.scopus.com/inward/record.url?scp=33748271948&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33748271948&partnerID=8YFLogxK

U2 - 10.1002/prot.21092

DO - 10.1002/prot.21092

M3 - Article

VL - 65

SP - 124

EP - 135

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

SN - 0887-3585

IS - 1

ER -