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As part of the NCBI Information Engineering Branch, the Protein Classification and Structure Group provides an array of services in bioinformatics and computational approaches to protein classification, including:
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Bioinformatics |
Development of "computer-friendly" databases for conserved domains (CDD) and macromolecular structures (MMDB); development of retrieval software; and development of methods (e.g., VAST, RPS-BLAST, CDART, SPARCLE) to identify associations among the data as part of the broader NCBI effort to facilitate biological discovery. |
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Protein Classification |
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CDD curation project for conserved domains provides insights into how patterns of residue conservation and divergence in a family relate to functional properties, and insights into sequence/structure/function relationships.
A companion tool, SPARCLE, the Subfamily Protein Architecture Labeling Engine, is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic conserved domain architecture. more... |
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3D Visualization |
Visualization and analysis of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures with the original Cn3D standalone software program, and the newer iCn3D WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the web, without the need to install a separate application. more... |
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3D Structure Comparisons |
Development of the VAST algorithm and VAST Search tool to identify similar 3D structures based on geometric methods; application of the algorithm on all publicly available, experimentally resolved protein structures in order to identify structures that are similar in shape, regardless of their degree of sequence similarity. more... |
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Previous work by the group, as part of the NCBI Computational Biology Branch (CBB), included the services above as well as the following research areas:
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Bioinformatics |
In addition to the ongoing bioinformatics work above, previous work included development of "computer-friendly" databases small molecules and their biological properties (PubChem) and biological systems (BioSystems). As a result of growth in the small molecules resources, those resources have branched off into a parallel group (Chemistry) in the Information Engineering Branch and continue to be available. |
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Biomolecular Interactions |
Analysis of interactions that have been observed across numerous experimentally determined 3D macromolecular structures in order to identify interaction sites, and to characterize and infer common types of interactions observed among homologous structures, particularly interactions between proteins and other biopolymers or chemicals (IBIS). more... |
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Cheminformatics |
Development of algorithms to compute, compare, and analyze the structure and physicochemical and biological properties of chemicals in the PubChem databases. As a result of growth in the small molecules resources, those resources have branched off into a parallel group (Chemistry) in the Information Engineering Branch and continue to be available. more... |
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Threading |
Development of algorithms for Protein Knowledge Base (PKB), a suite of software programs (written in the Splus language) for the convenient study and analysis of biomolecular structure data, including programs for protein fold recognition ("threading"). more... |
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