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Surprising similarities in structure comparison.
TLDR
Fast similarity-search algorithms are fast enough to have effectively removed the computer-time limitation for structure-structure search and alignment, and have made it possible to conduct systematic comparisons of all publicly available structures. Expand
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Threading a database of protein cores
We present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”1 The sequences of these proteins are notExpand
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MMDB and VAST+: tracking structural similarities between macromolecular complexes
TLDR
The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Expand
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IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
TLDR
We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Expand
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MMDB: Entrez's 3D structure database
TLDR
We focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. Expand
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MMDB: annotating protein sequences with Entrez's 3D-structure database
TLDR
We present an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links, with the Molecular Modeling Database (MMDB), a 3D-structure database. Expand
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MMDB: 3D structures and macromolecular interactions
TLDR
We present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. Expand
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Threading analysis suggests that the obese gene product may be a helical cytokine
The ob gene encodes a protein that, in mutant form, is associated with obesity and type II diabetes in mice. Sequence analysis has revealed no similarities to other proteins, however, and no clues asExpand
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Homology Inference of Protein-Protein Interactions via Conserved Binding Sites
The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists,Expand
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Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.
A large set of three-dimensional structures of 264 protein-protein complexes with known nonsynonymous single nucleotide polymorphisms (nsSNPs) at the interface was built using homology-based methods.Expand
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