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Surprising similarities in structure comparison.
- J. Gibrat, T. Madej, S. Bryant
- Computer Science, Medicine
- Current opinion in structural biology
- 1 June 1996
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
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 not… Expand
MMDB and VAST+: tracking structural similarities between macromolecular complexes
- T. Madej, C. Lanczycki, +4 authors S. Bryant
- Biology, Computer Science
- Nucleic Acids Res.
- 5 December 2013
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
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
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
MMDB: Entrez's 3D structure database
- A. Marchler-Bauer, K. J. Addess, +5 authors S. Bryant
- Medicine, Computer Science
- Nucleic Acids Res.
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
MMDB: annotating protein sequences with Entrez's 3D-structure database
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
MMDB: 3D structures and macromolecular interactions
We present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. Expand
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 as… Expand
Homology Inference of Protein-Protein Interactions via Conserved Binding Sites
- Manoj Tyagi, Ratna R. Thangudu, D. Zhang, S. Bryant, T. Madej, A. Panchenko
- Biology, Medicine
- PloS one
- 31 January 2012
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
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