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Updated: Jul 5, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Active site profiling to identify protein functional sites in sequences and structures using the Deacon Active Site
1Wake Forest University, Winston-Salem, North Carolina.
Current Protocols in Bioinformatics
|April 23, 2008
Summary
The DASP web application aids in analyzing protein functional sites by creating active site profiles. This tool helps identify common and unique features within protein families for detailed functional site characterization.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Detailed characterization of protein functional sites is crucial and requires advanced analytical methods.
- Existing methods for protein functional site analysis are under active development, highlighting a need for improved tools.
Purpose of the Study:
- To describe the DASP (Database for Annotation, Soaking, and PDB) web application for protein functional site analysis.
- To present two protocols for utilizing DASP to create active site profiles and identify functional site signatures.
Main Methods:
- Development and description of the DASP web application based on a previously established method.
- Protocol 1: Creation of functional site signatures and active site profiles from protein structures.
- Protocol 2: Using active site profiles to search for similar functional sites in protein sequences.
Main Results:
- The DASP application enables the generation of detailed active site profiles for any protein family.
- Analysis of profiles reveals conserved features across families and unique characteristics (specificity determinants) within subfamilies.
- The tool facilitates searching for novel sequences containing functional sites similar to known ones.
Conclusions:
- DASP provides a valuable resource for the detailed annotation and analysis of protein functional sites.
- The presented protocols offer a systematic approach to understanding protein family-specific functional site characteristics and discovering related sequences.
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