Molecular Modeling Database
Names
More detailed information about this field from each metasource.
Molecular Modeling Database
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
NCBI Structure
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
mmdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
Names
More detailed information about this field from each metasource.
Molecular Modeling Database
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
NCBI Structure
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
mmdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
Other names: MMDB, NCBI Structure, mmdb
Names
More detailed information about this field from each metasource.
Molecular Modeling Database
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
NCBI Structure
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
mmdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.
Description
More detailed information about this field from each metasource.
The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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 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: (1) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (2) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (3) 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/query.fcgi?db=Structure.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
Database of molecular modelling of 3-D structures; experimentally determined structures only.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
Webpage:
https://www.ncbi.nlm.nih.gov/structureWebpage
More detailed information about this field from each metasource.
https://www.ncbi.nlm.nih.gov/structure
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
http://www.ncbi.nlm.nih.gov/Structure/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
Licence:
Name: NCBI Website and Data Usage Policies and DisclaimersLicence name
More detailed information about this field from each metasource.
NCBI Website and Data Usage Policies and Disclaimers
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://www.ncbi.nlm.nih.gov/home/about/policies/
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://www.ncbi.nlm.nih.gov/About/disclaimer.html
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
MMDB and VAST+: tracking structural similarities between macromolecular complexes
PMID: 24319143
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB: annotating protein sequences with Entrez's 3D-structure database
PMID: 17135201
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB: Entrez's 3D-structure database
PMID: 12520055
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
MMDB: 3D structures and macromolecular interactions
PMID: 22135289
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
http://dx.doi.org/10.1093/nar/GKR1162
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
MMDB and VAST+: tracking structural similarities between macromolecular complexes
PMID: 24319143
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB: annotating protein sequences with Entrez's 3D-structure database
PMID: 17135201
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MMDB: Entrez's 3D-structure database
PMID: 12520055
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
MMDB: 3D structures and macromolecular interactions
PMID: 22135289
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
http://dx.doi.org/10.1093/nar/GKR1162
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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MMDB and VAST+: tracking structural similarities between macromolecular complexes
PubMed citations: 99.
99 articles citing: MMDB and VAST+: tracking structural similarities between macromolecular complexes
A novel circular RNA, circIgfbp2, links neural plasticity and anxiety through targeting mitochondrial dysfunction and oxidative stress-induced synapse dysfunction after traumatic brain injury. PMID:35918398
Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis. PMID:35731824
Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean. PMID:35684171
Dali server: structural unification of protein families. PMID:35610055
Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease Activities. PMID:35566194
In Silico Approaches to Identify Polyphenol Compounds as α-Glucosidase and α-Amylase Inhibitors against Type-II Diabetes. PMID:34944521
Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases. PMID:34928179
In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. PMID:34920161
Calsequestrin 1 Is an Active Partner of Stromal Interaction Molecule 2 in Skeletal Muscle. PMID:34831044
Discovering the Ultimate Limits of Protein Secondary Structure Prediction. PMID:34827624
Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires. PMID:34646268
Probing the Role of bba30, a Highly Conserved Gene of the Lyme Disease Spirochete, Throughout the Mouse-Tick Infectious Cycle. PMID:34581605
Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. PMID:34572502
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry. PMID:34520740
Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates. PMID:34339281
3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. PMID:34083757
To Ubiquitinate or Not to Ubiquitinate: TRIM17 in Cell Life and Death. PMID:34069831
Annexins and Membrane Repair Dysfunctions in Muscular Dystrophies. PMID:34067866
Nitric Oxide and Electrophilic Cyclopentenone Prostaglandins in Redox signaling, Regulation of Cytoskeleton Dynamics and Intercellular Communication. PMID:34026763
Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver. PMID:33997819
Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2. PMID:33923919
Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2. PMID:33669738
Identification of a unique endoplasmic retention motif in the Xenopus GIRK5 channel and its contribution to oocyte maturation. PMID:33565726
Calsequestrin: a well-known but curious protein in skeletal muscle. PMID:33288873
PubChem in 2021: new data content and improved web interfaces. PMID:33151290
Biophysical analysis of SARS-CoV-2 transmission and theranostic development via N protein computational characterization. PMID:33118327
Evolutionary aspects of the Viridiplantae nitroreductases. PMID:33025290
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
Real time structural search of the Protein Data Bank. PMID:32639954
Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. PMID:32637961
Reversible Oxidative Modifications in Myoglobin and Functional Implications. PMID:32599765
An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. PMID:32523014
Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials. PMID:32489400
In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus. PMID:32485894
TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. PMID:32479639
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. PMID:32392302
Caretta - A multiple protein structure alignment and feature extraction suite. PMID:32368333
Erlotinib sensitivity of MAPK1p.D321N mutation in head and neck squamous cell carcinoma. PMID:32351709
IL28A protein homotetramer structure is required for autolysosomal degradation of HCV-NS5A in vitro. PMID:32205851
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete. PMID:32157997
Pyocin S5 Import into Pseudomonas aeruginosa Reveals a Generic Mode of Bacteriocin Transport. PMID:32156826
PA0335, a Gene Encoding Histidinol Phosphate Phosphatase, Mediates Histidine Auxotrophy in Pseudomonas aeruginosa. PMID:31862725
Crystal structure of a Vip3B family insecticidal protein reveals a new fold and a unique tetrameric assembly. PMID:31840313
Urea Derivatives in Modern Drug Discovery and Medicinal Chemistry. PMID:31789518
Structural Conservation and Diversity of PilZ-Related Domains. PMID:31740493
Arf-GEF localization and function at myosin-rich adherens junctions via coiled-coil heterodimerization with an adaptor protein. PMID:31693432
Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. PMID:31628659
A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. PMID:31522888
Molecular interaction site on procoagulant myosin for factor Xa-dependent prothrombin activation. PMID:31481465
Thyroid Hormone Distributor Proteins During Development in Vertebrates. PMID:31440205
PUG-View: programmatic access to chemical annotations integrated in PubChem. PMID:31399858
3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns. PMID:31261733
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. PMID:31218344
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. PMID:31172379
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. PMID:31114904
Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor. PMID:31113879
Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. PMID:30945220
Identification of a Recombinant Human Interleukin-12 (rhIL-12) Fragment in Non-Reduced SDS-PAGE. PMID:30925680
Serum protein expression in Equine Glandular Gastric Disease (EGGD) induced by phenylbutazone. PMID:30674748
Mycobacterium tuberculosis SatS is a chaperone for the SecA2 protein export pathway. PMID:30604681
A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro. PMID:30499668
PubChem 2019 update: improved access to chemical data. PMID:30371825
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Protein AMPylation by an Evolutionarily Conserved Pseudokinase. PMID:30270044
Fast design of arbitrary length loops in proteins using InteractiveRosetta. PMID:30249181
Proteomic determination of the lysine acetylome and phosphoproteome in the rat native inner medullary collecting duct. PMID:29932826
A Hyperthermophilic Phage Decoration Protein Suggests Common Evolutionary Origin with Herpesvirus Triplex Proteins and an Anti-CRISPR Protein. PMID:29779790
Exploring the binding sites and binding mechanism for hydrotrope encapsulated griseofulvin drug on γ-tubulin protein. PMID:29324869
The Combined Use of in Silico, in Vitro, and in Vivo Analyses to Assess Anti-cancerous Potential of a Bioactive Compound from Cyanobacterium Nostoc sp. MGL001. PMID:29230175
Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea. PMID:29208747
Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. PMID:28784764
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. PMID:28459991
Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. PMID:28449100
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PMID:27893862
Establishing a reference array for the CS-αβ superfamily of defensive peptides. PMID:27863510
The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation. PMID:27602573
Getting the most out of PubChem for virtual screening. PMID:27454129
Hexokinase Is an Innate Immune Receptor for the Detection of Bacterial Peptidoglycan. PMID:27374331
Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review. PMID:27301744
Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation. PMID:27298344
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
Independent Evolution of Six Families of Halogenating Enzymes. PMID:27153321
Dissecting the structural basis of MEIG1 interaction with PACRG. PMID:26726850
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. PMID:26699921
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. PMID:26493835
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
Partial protein domains: evolutionary insights and bioinformatics challenges. PMID:25986583
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. PMID:25811853
Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns. PMID:25657820
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
CDD: NCBI's conserved domain database. PMID:25414356
Database resources of the National Center for Biotechnology Information. PMID:25398906
Exploring the evolutionary route of the acquisition of betaine aldehyde dehydrogenase activity by plant ALDH10 enzymes: implications for the synthesis of the osmoprotectant glycine betaine. PMID:24884441
Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. PMID:24548880
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579 -
MMDB: annotating protein sequences with Entrez's 3D-structure database
PubMed citations: 61.
61 articles citing: MMDB: annotating protein sequences with Entrez's 3D-structure database
Orf165 is associated with cytoplasmic male sterility in pepper. PMID:34555144
Genetic analysis of a congenital split‑hand/split‑foot malformation 4 pedigree. PMID:29620206
Characterization of the complex involved in regulating V-ATPase activity of the vacuolar and endosomal membrane. PMID:28643238
Suppression and synthetic-lethal genetic relationships of ΔgpsB mutations indicate that GpsB mediates protein phosphorylation and penicillin-binding protein interactions in Streptococcus pneumoniae D39. PMID:28010038
Substrate and Cofactor Range Differences of Two Cysteine Dioxygenases from Ralstonia eutropha H16. PMID:26590284
Evidence-Based Structural Model of the Staphylococcal Repressor Protein: Separation of Functions into Different Domains. PMID:26414067
Isolation and characterization of a β-propeller gene containing phosphobacterium Bacillus subtilis strain KPS-11 for growth promotion of potato (Solanum tuberosum L.). PMID:26106383
Fap2 of Fusobacterium nucleatum is a galactose-inhibitable adhesin involved in coaggregation, cell adhesion, and preterm birth. PMID:25561710
PubChem3D: conformer ensemble accuracy. PMID:23289532
Clostridial binary toxins: iota and C2 family portraits. PMID:22919577
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PMID:22815919
Overcoming sequence misalignments with weighted structural superposition. PMID:22733542
Cytoplasmic amino acids within the membrane interface region influence connexin oligomerization. PMID:22722762
Annotation of functional sites with the Conserved Domain Database. PMID:22434827
The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response. PMID:22407319
Osteophilic multilayer coatings for accelerated bone tissue growth. PMID:22311551
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities. PMID:22266938
Calcineurin homologous protein: a multifunctional Ca2+-binding protein family. PMID:22189947
Database resources of the National Center for Biotechnology Information. PMID:22140104
MMDB: 3D structures and macromolecular interactions. PMID:22135289
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. PMID:22102591
The invention of WUS-like stem cell-promoting functions in plants predates leptosporangiate ferns. PMID:22076631
Specificity of interaction between clostridium perfringens enterotoxin and claudin-family tight junction proteins. PMID:22069652
Divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases. PMID:22069329
Divergence and convergence in enzyme evolution. PMID:22069324
The Histone Database: an integrated resource for histones and histone fold-containing proteins. PMID:22025671
OPM database and PPM web server: resources for positioning of proteins in membranes. PMID:21890895
PubChem3D: Similar conformers. PMID:21554721
PubChem3D: Conformer generation. PMID:21272340
FcRn overexpression in mice results in potent humoral response against weakly immunogenic antigen. PMID:21239891
Database resources of the National Center for Biotechnology Information. PMID:21097890
Frequent mutation of BAP1 in metastasizing uveal melanomas. PMID:21051595
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. PMID:21048085
Unexploited therapies in breast and prostate cancer: blockade of the prolactin receptor. PMID:20846877
A novel minicollagen gene links cnidarians and myxozoans. PMID:20810433
A genomic glance at the components of the mRNA export machinery in Plasmodium falciparum. PMID:20798816
Novel roles of the picornaviral 3D polymerase in viral pathogenesis. PMID:20625447
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Functional states of homooligomers: insights from the evolution of glycosyltransferases. PMID:20381499
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family. PMID:20157477
Granzyme B cleavage of autoantigens in autoimmunity. PMID:20075942
The WUS homeobox-containing (WOX) protein family. PMID:20067590
Polygalacturonase inhibiting protein: isolation, developmental regulation and pathogen related expression in Panax ginseng C.A. Meyer. PMID:19946753
An overview of the PubChem BioAssay resource. PMID:19933261
Structure, affinity, and availability of estrogen receptor complexes in the cellular environment. PMID:19926790
GenBank. PMID:19910366
Database resources of the National Center for Biotechnology Information. PMID:19910364
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. PMID:19906708
In silico cloning, expression of Rieske-like apoprotein gene and protein subcellular localization in the Pacific oyster, Crassostrea gigas. PMID:19876765
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. PMID:19843613
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. PMID:19706177
An insight into the transcriptome and proteome of the salivary gland of the stable fly, Stomoxys calcitrans. PMID:19576987
Structural and mechanistic insights into the association of PKCalpha-C2 domain to PtdIns(4,5)P2. PMID:19346474
GenBank. PMID:18940867
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Database resources of the National Center for Biotechnology Information. PMID:18940862
Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner. PMID:18922021
SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. PMID:18811932
GenBank. PMID:18073190
Database resources of the National Center for Biotechnology Information. PMID:18045790 -
MMDB: Entrez's 3D-structure database
PubMed citations: 53.
53 articles citing: MMDB: Entrez's 3D-structure database
Epitope analysis of anti-myeloperoxidase antibodies in patients with ANCA-associated vasculitis. PMID:23577119
PubChem3D: conformer ensemble accuracy. PMID:23289532
Cytoplasmic amino acids within the membrane interface region influence connexin oligomerization. PMID:22722762
Homology inference of protein-protein interactions via conserved binding sites. PMID:22303436
Modulating protein-protein interactions with small molecules: the importance of binding hotspots. PMID:22198293
Specificity of interaction between clostridium perfringens enterotoxin and claudin-family tight junction proteins. PMID:22069652
A gain-of-function germline mutation in Drosophila ras1 affects apoptosis and cell fate during development. PMID:21858158
PubChem3D: Conformer generation. PMID:21272340
FcRn overexpression in mice results in potent humoral response against weakly immunogenic antigen. PMID:21239891
Protein structure databases. PMID:21225378
Novel roles of the picornaviral 3D polymerase in viral pathogenesis. PMID:20625447
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Cystatin superfamily. PMID:20173285
Granzyme B cleavage of autoantigens in autoimmunity. PMID:20075942
Structure, affinity, and availability of estrogen receptor complexes in the cellular environment. PMID:19926790
Determination of the active site of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone dioxygenase (PcpA). PMID:19924449
In silico cloning, expression of Rieske-like apoprotein gene and protein subcellular localization in the Pacific oyster, Crassostrea gigas. PMID:19876765
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. PMID:19843613
Exploring functional roles of multibinding protein interfaces. PMID:19591200
Improving protein structure similarity searches using domain boundaries based on conserved sequence information. PMID:19454035
OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries. PMID:19026662
Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. PMID:19023120
PDBsum new things. PMID:18996896
Tetanus toxin C fragment-conjugated nanoparticles for targeted drug delivery to neurons. PMID:17854886
Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. PMID:17569521
Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins. PMID:17425794
HLAMatchmaker: a molecularly based algorithm for histocompatibility determination. V. Eplet matching for HLA-DR, HLA-DQ, and HLA-DP. PMID:17207708
Database resources of the National Center for Biotechnology Information. PMID:17170002
Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. PMID:17151104
MMDB: annotating protein sequences with Entrez's 3D-structure database. PMID:17135201
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. PMID:17135193
State of the art: refinement of multiple sequence alignments. PMID:17105653
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. PMID:17065464
Adenoviral gene therapy, radiation, and prostate cancer. PMID:16985830
Immunoinformatics comes of age. PMID:16846250
Refining multiple sequence alignments with conserved core regions. PMID:16707662
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. PMID:16630345
Domain-based small molecule binding site annotation. PMID:16545112
Investigating the local flexibility of functional residues in hemoproteins. PMID:16428284
Evolutionary plasticity of protein families: coupling between sequence and structure variation. PMID:16184609
Insect chitin synthases: a review. PMID:16075270
A single amino acid converts a repressor to an activator of flowering. PMID:15894619
Characterization of herpes simplex virus type 1 thymidine kinase mutants selected under a single round of high-dose brivudin. PMID:15827202
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes. PMID:15498941
Analysis of protein homology by assessing the (dis)similarity in protein loop regions. PMID:15382231
CaspR: a web server for automated molecular replacement using homology modelling. PMID:15215460
LEON: multiple aLignment Evaluation Of Neighbours. PMID:14982955
DomIns: a web resource for domain insertions in known protein structures. PMID:14681392
Database resources of the National Center for Biotechnology Information: update. PMID:14681353
GenBank: update. PMID:14681350
CDD: a curated Entrez database of conserved domain alignments. PMID:12520028
Database resources of the National Center for Biotechnology. PMID:12519941 -
MMDB: 3D structures and macromolecular interactions
PubMed citations: 47.
47 articles citing: MMDB: 3D structures and macromolecular interactions
Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. PMID:32637961
Tick-borne encephalitis virus (TBEV) prevalence in field-collected ticks (Ixodes ricinus) and phylogenetic, structural and virulence analysis in a TBE high-risk endemic area in southwestern Germany. PMID:32527288
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
Characterization of a sandwich ELISA for quantification of total human soluble neuropilin-1. PMID:31219204
Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. PMID:30945220
Isolation of a high-affinity Bet v 1-specific IgG-derived ScFv from a subject vaccinated with hypoallergenic Bet v 1 fragments. PMID:29315611
Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites. PMID:28158543
Suppression and synthetic-lethal genetic relationships of ΔgpsB mutations indicate that GpsB mediates protein phosphorylation and penicillin-binding protein interactions in Streptococcus pneumoniae D39. PMID:28010038
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. PMID:27872662
Database resources of the National Center for Biotechnology Information. PMID:26615191
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. PMID:26213149
Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli. PMID:25953406
Fitness profiling links topoisomerase II regulation of centromeric integrity to doxorubicin resistance in fission yeast. PMID:25669599
Amoebal endosymbiont Parachlamydia acanthamoebae Bn9 can grow in immortal human epithelial HEp-2 cells at low temperature; an in vitro model system to study chlamydial evolution. PMID:25643359
High-density IgE recognition of the major grass pollen allergen Phl p 1 revealed with single-chain IgE antibody fragments obtained by combinatorial cloning. PMID:25637023
Clinical and genetic investigation of a multi-generational Chinese family afflicted with Von Hippel-Lindau disease. PMID:25563310
Database resources of the National Center for Biotechnology Information. PMID:25398906
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PMID:25375667
The biosynthesis of UDP-d-FucNAc-4N-(2)-oxoglutarate (UDP-Yelosamine) in Bacillus cereus ATCC 14579: Pat and Pyl, an aminotransferase and an ATP-dependent Grasp protein that ligates 2-oxoglutarate to UDP-4-amino-sugars. PMID:25368324
Bioactive proteins and peptides isolated from Chinese medicines with pharmaceutical potential. PMID:25067942
B-cell epitopes in GroEL of Francisella tularensis. PMID:24968190
Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PMID:24931138
Amoebal endosymbiont Neochlamydia genome sequence illuminates the bacterial role in the defense of the host amoebae against Legionella pneumophila. PMID:24747986
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Synthetic lethality in the tobacco plastid ribosome and its rescue at elevated growth temperatures. PMID:24563204
The PhoU protein from Escherichia coli interacts with PhoR, PstB, and metals to form a phosphate-signaling complex at the membrane. PMID:24563032
Computational large-scale mapping of protein-protein interactions using structural complexes. PMID:24510594
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Variant non ketotic hyperglycinemia is caused by mutations in LIAS, BOLA3 and the novel gene GLRX5. PMID:24334290
MMDB and VAST+: tracking structural similarities between macromolecular complexes. PMID:24319143
Database resources of the National Center for Biotechnology Information. PMID:24259429
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
Discovery of protective B-cell epitopes for development of antimicrobial vaccines and antibody therapeutics. PMID:24219801
Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. PMID:24164321
Mutation of fibulin-1 causes a novel syndrome involving the central nervous system and connective tissues. PMID:24084572
To fuse or not to fuse: what is your purpose? PMID:24038604
The other face of restriction: modification-dependent enzymes. PMID:23990325
The staphylococcal enterotoxin (SE) family: SEB and siblings. PMID:23959032
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Role of pore-forming toxins in bacterial infectious diseases. PMID:23699254
Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases. PMID:23446356
PubChem3D: conformer ensemble accuracy. PMID:23289532
CDD: conserved domains and protein three-dimensional structure. PMID:23197659
Database resources of the National Center for Biotechnology Information. PMID:23193264
Identifying structural domains of proteins using clustering. PMID:23116496
Public domain databases for medicinal chemistry. PMID:22731701
Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins. PMID:22693546 - http://dx.doi.org/10.1093/nar/GKR1162
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More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
biology
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
genes
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
macromolecular structures
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
molecular modelling
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
structural biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biology
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
genes
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
macromolecular structures
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: NCBI Structure; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HS58 last accessed: 2022-11-04
molecular modelling
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
structural biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:09.791462
dna modeling and simulation molecular interaction molecular structure protein small molecule structure structure protein structure gene macromolecular structures proteins molecular modelling structural biology structure analysis small molecule structure prediction
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