MMDB: Entrez's 3D-structure database

Jie Chen¹, John B Anderson, Carol DeWeese-Scott

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

|January 10, 2003

Abstract

None:

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, 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. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.

Related Experiment Videos

MMDB: Entrez's 3D-structure database

Related Concept Videos

MD2NMR: Linking molecular dynamics with NMR relaxation.

Integrating evidence from protein domains to identify cancer driver mutations.

G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.

Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability.

G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.

Deciphering Allosteric Modulation of Cancer-Associated Histone Missense Mutations.

AID self-assembly and multistranded DNA binding drive synapsis in class switch recombination.

Coronavirus NSP14 drives internal m7G modification to rewire host splicing and promote viral replication.

Insights into the recruitment of the H3K4me3 reader Spp1 by the meiotic double-strand break protein Mer2.

Newly synthesized histones: passive or active players in the regulation of epigenetic inheritance?

ETfinder: harnessing conserved C-terminal tails of single-stranded DNA-binding proteins for mining and engineering RecET systems in non-model microbial chassis.

MOSAIC enables selective transfer and fairness-aware generalization in cross-species DNA methylation prediction.

Siteomix: a PyMOL plugin for the detection, alignment, and similarity analysis of protein‒ligand binding sites.

Guardians of splicing: quality control mechanisms of snRNA variants.

A high-throughput strategy for screening umami peptides from Chouguiyu based on peptidomics and machine learning-assisted molecular simulation.

PregBase: A comprehensive knowledge base for clinically relevant knowledge representation and biomarker prediction in pregnancy.

Machine Learning Prediction and Experimental Validation of Antimicrobial Peptide Activity Differences against Gram-Positive and Gram-Negative Bacteria.

Comparative machine learning analysis identifies random forest and adaboost as superior models for the evaluation of semen quality and reproductive hormones.

Related Experiment Videos

MMDB: Entrez's 3D-structure database

None:

Related Concept Videos

Related Articles