Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
Open Access
- 1 January 2008
- journal article
- research article
- Published by Springer Nature in BMC Structural Biology
- Vol. 8 (1) , 45
- https://doi.org/10.1186/1472-6807-8-45
Abstract
Protein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role.Keywords
This publication has 69 references indexed in Scilit:
- Structure of an Amide Bond Forming F420:γγ-glutamyl Ligase from Archaeoglobus Fulgidus - A Member of a New Family of Non-ribosomal Peptide SynthasesJournal of Molecular Biology, 2007
- CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residuesNucleic Acids Research, 2006
- Structural Evolution of the Protein Kinase–Like SuperfamilyPLoS Computational Biology, 2005
- Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensionsActa Crystallographica Section D-Biological Crystallography, 2004
- Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface PatternsJournal of Molecular Biology, 2003
- Identification of protein biochemical functions by similarity search using the molecular surface database eF‐siteProtein Science, 2003
- Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine KinaseScience, 2000
- Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand designProtein Science, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- STRUCTURE-BASED INHIBITORS OF HIV-1 PROTEASEAnnual Review of Biochemistry, 1993