Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MMDB: 3D structure data in Entrez.

ABSTRACT: Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure-function properties. The goal of Entrez's 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez's search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline((R)), for example, and link to 3D structures reported in these articles. (ii) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view a combined molecular-graphic and alignment display, to infer approximate 3D structure. Entrez's MMDB (Molecular Modeling DataBase) may be accessed at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html

SUBMITTER: Wang Y

PROVIDER: S-EPMC102448 | biostudies-literature | 2000 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

MMDB: 3D structure data in Entrez.

Wang Y Y Addess K J KJ Geer L L Madej T T Marchler-Bauer A A Zimmerman D D Bryant S H SH

Nucleic acids research 20000101 1

Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure-function properties. The goal of Entrez's 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez's search engine provides three powerful features: (i) Links between databases; one may s ...[more]

PMID: 10592236

Similar Datasets

MMDB: Entrez's 3D-structure database.

Project description: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.

| S-EPMC165533 | biostudies-literature

MMDB: Entrez's 3D-structure database.

Project description:Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez's 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez's search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez's Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.

| S-EPMC99072 | biostudies-literature

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Project description:Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).

| S-EPMC1751549 | biostudies-literature

MMDB: 3D structures and macromolecular interactions.

Project description:Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

| S-EPMC3245041 | biostudies-literature

Physical and data structure of 3D genome.

Project description:With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi-self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.

| S-EPMC6954067 | biostudies-literature

Protein Data Bank: the single global archive for 3D macromolecular structure data.

Project description:The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

| S-EPMC6324056 | biostudies-literature

Advances in RNA 3D Structure Modeling Using Experimental Data.

Project description:RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.

| S-EPMC7649352 | biostudies-literature

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer.

Project description:The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: the full-length glycan composition, including linkage details for the glycosidic bonds. The developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

| S-EPMC7554661 | biostudies-literature

Dynamic alterations of 3D chromatin structure during differentiation

Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecting cis regulatory elements such as promoters and enhancers. However, the dynamics of these processes during cell differentiation still remains unclear. We used Tethered Chromatin Conformation Capture (TCC) to compare the three dimensional chromatin structure of mouse embryonic stem cells (ESC) and neural stem cells (NSC) which we directly derived from the ESC.

2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Project description: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. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

| S-EPMC3965051 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data