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As part of the NCBI Computational Biology Branch (CBB), scientists in the Structure group conduct basic research in bioinformatics and cheminformatics. Specific research areas include:
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Bioinformatics |
Development of "computer-friendly" databases for macromolecular structures (MMDB), conserved domains (CDD), small molecules and their biological properties (PubChem), and biological systems (BioSystems); development of retrieval software; and development of methods (e.g., VAST, RPS-BLAST, CDART) to identify associations among the data as part of the broader NCBI effort to facilitate biological discovery. more... |
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3D Visualization |
Visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures with the Cn3D software program. 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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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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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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Cheminformatics |
Development of algorithms to compute, compare, and analyze the structure and physicochemical and biological properties of chemicals in the PubChem databases. 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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