Protein Model Database
Names
More detailed information about this field from each metasource.
Protein Model Database
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
PMDB
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
PMDB - Protein Model Database
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
pmdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
Names
More detailed information about this field from each metasource.
Protein Model Database
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
PMDB
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
PMDB - Protein Model Database
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
pmdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
Other names: PMDB, PMDB - Protein Model Database, pmdb
Names
More detailed information about this field from each metasource.
Protein Model Database
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
PMDB
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
PMDB - Protein Model Database
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
pmdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.
Description
More detailed information about this field from each metasource.
The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Protein Model Database (PMDB) is a public resource aimed at storing manually built three-dimensional models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. The system allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
A tool collects three dimensional protein models obtained by structure prediction methods.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
Webpage:
http://srv00.recas.ba.infn.it/PMDB/main.phpWebpage
More detailed information about this field from each metasource.
http://srv00.recas.ba.infn.it/PMDB/main.php
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://bioinformatics.cineca.it/PMDB/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
Licence:
Name: PMDB Attribution requiredLicence name
More detailed information about this field from each metasource.
PMDB Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
http://srv00.recas.ba.infn.it/PMDB/help.php
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The PMDB Protein Model Database
PMID: 16381873
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkj105
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
Publications
More detailed information about this field from each metasource.
The PMDB Protein Model Database
PMID: 16381873
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkj105
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
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The PMDB Protein Model Database
PubMed citations: 107.
107 articles citing: The PMDB Protein Model Database
In silico structural, phylogenetic and drug target analysis of putrescine monooxygenase from Shewanella putrefaciens-95. PMID:35412199
Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PMID:35341049
Structural heterogeneity assessment among the isoforms of fungal 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase: a comparative in silico perspective. PMID:35103879
Molecular interaction of nitrate transporter proteins with recombinant glycinebetaine results in efficient nitrate uptake in the cyanobacterium Anabaena PCC 7120. PMID:34793479
Epitope-specific anti-PrP antibody toxicity: a comparative in-silico study of human and mouse prion proteins. PMID:34632945
A computational study on hydroxychloroquine binding to target proteins related to SARS-COV-2 infection. PMID:34458558
Computational study to discover potent phytochemical inhibitors against drug target, squalene synthase from Leishmania donovani. PMID:34141935
Heterologous expression of cyanobacterial PCS confers augmented arsenic and cadmium stress tolerance and higher artemisinin in Artemisia annua hairy roots. PMID:34122662
Structural characterization and in vitro lipid binding studies of non-specific lipid transfer protein 1 (nsLTP1) from fennel (Foeniculum vulgare) seeds. PMID:33277525
Genome-wide analysis of HSP90 gene family in the Mediterranean olive (Olea europaea subsp. europaea) provides insight into structural patterns, evolution and functional diversity. PMID:33268931
Applying computer simulations in battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic. PMID:33102687
Homology modeling and molecular dynamics based insights into Chalcone synthase and Chalcone isomerase in Phyllanthus emblica L. PMID:32832333
Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. PMID:32737682
Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. PMID:32296570
Computational prediction of active sites and ligands in different AHL quorum quenching lactonases and acylases. PMID:32020908
Establishment of the experimental procedure for prediction of conjugation capacity in mutant UGT1A1. PMID:31730632
Facilities that make the PDB data collection more powerful. PMID:31724231
Hierarchical-Clustering, Scaffold-Mining Exercises and Dynamics Simulations for Effectual Inhibitors Against Lipid-A Biosynthesis of Helicobacter pylori. PMID:31719913
Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels. PMID:31552786
Molecular modelling and docking of Mus musculus HMGB1 inflammatory protein with CGA. PMID:31485132
Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1. PMID:31457406
Cloning and Characterization of a Chondroitin AC Exolyase from Arthrobacter sp. SD-04. PMID:31444737
Identification of lead molecules against potential drug target protein MAPK4 from L. donovani: An in-silico approach using docking, molecular dynamics and binding free energy calculation. PMID:31425543
Biochemical and structural characterization of tyrosine aminotransferase suggests broad substrate specificity and a two-state folding mechanism in Leishmania donovani. PMID:31393078
Genome-wide mining of respiratory burst homologs and its expression in response to biotic and abiotic stresses in Triticum aestivum. PMID:31140145
Dynamic analysis of human tyrosinase intra-melanosomal domain and mutant variants to further understand oculocutaneous albinism type 1. PMID:30868138
Purification and Characterization of a Nonspecific Lipid Transfer Protein 1 (nsLTP1) from Ajwain (Trachyspermum ammi) Seeds. PMID:30858403
Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PMID:30540790
In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato. PMID:30405403
Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus. PMID:30402510
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database. PMID:30052959
Molecular modeling, docking and protein-protein interaction analysis of MAPK signalling cascade involved in Camalexin biosynthesis in Brassica rapa. PMID:29983484
Computational prediction of vaccine potential epitopes and 3-dimensional structure of XAGE-1b for non-small cell lung cancer immunotherapy. PMID:29866600
A new insight into identification of in silico analysis of natural compounds targeting GPR120. PMID:29780684
Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the in silico approach. PMID:29745301
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PMID:29709017
The ins and outs of vesicular monoamine transporters. PMID:29666153
Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function. PMID:28894144
Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach. PMID:28611792
Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India. PMID:28264652
Insights using the molecular model of Lipoxygenase from Finger millet (Eleusine coracana (L.)). PMID:28149050
Cation Interactions and Membrane Potential Induce Conformational Changes in NaPi-IIb. PMID:27602725
CryGetter: a tool to automate retrieval and analysis of Cry protein data. PMID:27578522
In silico Prediction and Docking of Tertiary Structure of LuxI, an Inducer Synthase of Vibrio fischeri. PMID:27536699
Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses. PMID:27013796
Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking. PMID:26981117
The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism. PMID:26828963
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. PMID:26573537
Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. PMID:26388773
3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing. PMID:25860348
Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M. PMID:25848225
Optimal ligand descriptor for pocket recognition based on the Beta-shape. PMID:25835497
Computational identification and binding analysis of orphan human cytochrome P450 4X1 enzyme with substrates. PMID:25595103
Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: a computational study. PMID:25581715
Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H. PMID:25381619
Titanium dioxide nanoparticles as guardian against environmental carcinogen benzo[alpha]pyrene. PMID:25215666
Understanding the interaction determinants of CAPN1 inhibition by CAST4 from bovines using molecular modeling techniques. PMID:25215589
Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera. PMID:25085038
Molecular modeling of the Plasmodium falciparum pre-mRNA splicing and nuclear export factor PfU52. PMID:24861003
Homology modeling study of bovine μ-calpain inhibitor-binding domains. PMID:24806345
Genome wide survey and molecular modeling of hypothetical proteins containing 2Fe-2S and FMN binding domains suggests Rieske Dioxygenase Activity highlighting their potential roles in bioremediation. PMID:24616557
Computational studies on sirtuins from Trypanosoma cruzi: structures, conformations and interactions with phytochemicals. PMID:24551254
Flexible gates generate occluded intermediates in the transport cycle of LacY. PMID:24513108
In silico modeling and functional interpretations of Cry1Ab15 toxin from Bacillus thuringiensis BtB-Hm-16. PMID:24228249
in-silico characterization of β-(1, 3)-endoglucanase (ENGL1) from Aspergillus fumigatus by homology modeling and docking studies. PMID:24143049
Exploring N(1)-p-fluorobenzyl-cymserine as an inhibitor of 5-lipoxygenase as a candidate for type 2 diabetes and neurodegenerative disorder treatment. PMID:24059322
Molecular models and mutational analyses of plant specifier proteins suggest active site residues and reaction mechanism. PMID:23999604
Evolution of the key alkaloid enzyme putrescine N-methyltransferase from spermidine synthase. PMID:23908659
Computational protein structure modeling and analysis of UV-B stress protein in Synechocystis PCC 6803. PMID:23904742
Homology modeling and structural comparison of leucine rich repeats of Toll like receptors 1-10 of ruminants. PMID:23812948
Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate. PMID:23666632
Gene identification and comparative molecular modeling of a Trypanosoma rangeli major surface protease. PMID:23584556
The activity of prolactin releasing peptide correlates with its helicity. PMID:23426574
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. PMID:23360998
Analysis of multi-domain hypothetical proteins containing iron-sulphur clusters and fad ligands reveal rieske dioxygenase activity suggesting their plausible roles in bioremediation. PMID:23275712
Homology Modeling and Functional Characterization of PR-1a Protein of Hordeum vulgare subsp. Vulgare. PMID:23139589
"SP-G", a putative new surfactant protein--tissue localization and 3D structure. PMID:23094088
Homology modeling and functional annotation of bubaline pregnancy associated glycoprotein 2. PMID:22958467
Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae. PMID:22745763
Disulphide bridges of phospholipase C of Chlamydomonas reinhardtii modulates lipid interaction and dimer stability. PMID:22737232
Structure based virtual screening of novel inhibitors against multidrug resistant superbugs. PMID:22715312
Modeling of the Full-Size 3D Structure of Human Chaperone Hsp70 and Study of Its Interdomain Interactions. PMID:22649666
Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling. PMID:22493521
How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. PMID:22435086
Comparative modeling and molecular docking of orphan human CYP4V2 protein with fatty acid substrates: Insights into substrate specificity. PMID:22355237
Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237. PMID:22355225
Homology modeling of an antifungal metabolite plipastatin synthase from the Bacillus subtilis 168. PMID:22347779
Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis. PMID:22244187
Molecular modeling and identification of substrate binding site of orphan human cytochrome P450 4F22. PMID:22102778
Evaluation of model quality predictions in CASP9. PMID:21997462
Comprehensively surveying structure and function of RING domains from Drosophila melanogaster. PMID:21912646
Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain. PMID:21866316
Structure prediction and functional characterization of secondary metabolite proteins of Ocimum. PMID:21769194
Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase. PMID:21566738
Molecular modeling of human alkaline sphingomyelinase. PMID:21544170
Identification of potential Leptospira phosphoheptose isomerase inhibitors through virtual high-throughput screening. PMID:21382593
On the mechanism of chloroquine resistance in Plasmodium falciparum. PMID:21124966
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots. PMID:21029427
Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues. PMID:20979597
A ClpP protein model as tuberculosis target for screening marine compounds. PMID:20975890
Functionally important amino acids in the Arabidopsis thylakoid phosphate transporter: homology modeling and site-directed mutagenesis. PMID:20565143
Bomapin is a redox-sensitive nuclear serpin that affects responsiveness of myeloid progenitor cells to growth environment. PMID:20433722
Probing ligand binding modes of Mycobacterium tuberculosis MurC ligase by molecular modeling, dynamics simulation and docking. PMID:19484275
Analysis of oligomeric proteins during unfolding by pH and temperature. PMID:19205760
The evaluation of protein structure prediction results. PMID:18071927
Evidence for myxobacterial origin of eukaryotic defensins. PMID:18058146
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU. PMID:17116251 - http://dx.doi.org/10.1093/nar/gkj105
Tags:
Tags
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molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.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
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.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
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:04.198758
Tags
More detailed information about this field from each metasource.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.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
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PMDB; Protein Model Database; DOI: https://doi.org/10.25504/FAIRsharing.wkaakq; Last edited: April 26, 2021, 11:30 a.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
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
protein structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:04.198758
molecular structure protein protein structure structure structure structure prediction protein structure analysis
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