“…The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. …”
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“…project=pmdb-bq&d=pmdb).…”
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“…Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. …”
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“…In addition, the PainMonit Database (PMDB), a new dataset including both objective and subjective annotations for heat-induced pain in 52 subjects, is introduced. …”
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“…Predicted and best evaluated model has been successfully deposited to PMDB database with PMDB ID PM0078035. Active site identification revealed GLU(369), ALA(370), LEU(371), THR(372), HIS(373), LEU(374), HIS(376), SER(377), HIS(378), THR(385), LEU(389), HIS(394), PHE(399), LYS(400), LEU(401), ILE(403) and PRO(404) residues may play a major role during protein-protein, protein-drug and protein-cofactor interactions. …”
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“…The nucleotide sequence of Finger millet SBE was submitted to NCBI with the accession no KY648913 and protein structure of SBE of finger millet was also submitted in PMDB with the PMDB id - PM0080938. This research presents a comparative overview of Finger millet SBE and includes their properties, structural and functional characteristics, and recent developments on their post-translational regulation.…”
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“…The predicted tertiary structure of the native TRPS1 after refinement and validation was successfully submitted to the Protein Model Database and was assigned with PMDB ID PM0077843, as it was previously unpredicted. …”
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“…We report the sequence (GenBank accession number KY648917) and the structural model of finger millet starch synthase (PMDB ID: PM0081600).…”
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“…The structures are finally submitted in Protein Model Database, PMDB so that they become accessible to other users for further studies.…”
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“…The predicted model submitted in Protein Model Database, PMDB for public use. This model will be used in wide range of studies for functional analysis and improvement activity of the protein.…”
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“…Experimental results were obtained through several and rigorous cross-dataset tests, exploiting three well-known datasets, namely PMDB, MorphDB, and AMSL, containing automatic and manually refined facial morphed images, showing that the proposed framework was able to achieve satisfying results.…”
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“…The validated 3D structure of seed protein was then successfully submitted to the Protein Model Database and was assigned with the PMDB ID PM0077829. All the predicted structures were superimposed with a root mean square deviation value of 7.0 Å and a high Dali Z-score of 1.9. …”
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“…The structure of BmGST was modeled using modeller9v10 and was submitted to PMDB. Molecular docking study reveals arbindazole to be the most potent compounds against GST from both the filarial parasites. …”
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“…The computed model's energy was minimized and validated using PROCHECK and Errat tool to obtain a stable model structure and was submitted in Protein Model Database (PMDB-ID: PM0079251). Stable model was used for molecular docking against Risperidone and their 15 derivatives using AutoDock 4.2, which resulted in energy-based descriptors such as Binding Energy, Ligand Efficiency, Inhib Constant, Intermol energy, vdW + Hbond + desolv Energy, Electrostatic Energy, Total Internal Energy and Torsional Energy. …”
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“…The modelled structure was deposited in the protein model database with PMDB ID: PM0080988. Molecular dynamic simulation of the enzyme-inhibitor complex along with the free energy calculations over 50 ns showed that GEN and CHY are more stable in their binding. …”
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“…DATABASE: Model data are available in the PMDB database under the accession number PM0080780.…”
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“…The computed model's energy was minimized and validated using PROCHECK to obtain a stable model structure and is submitted in Protein Model Database (PMDB-ID: PM0075741). Stable model was further used for virtual screening against marine derived bioactive compound database through molecular docking studies using AutoDock 3.05. …”
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“…Built tertiary protein models designated as ACCNK1–ACCNK40 have been deposited in the PMDB with accessions PM0083418–39 and PM0083476–93. …”
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“…The compounds were identified based on data retrieved from the PMDB databases according to the accurate mass number, secondary fragment, and isotope distribution. …”
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