The PMDB Protein Model Database

Castrignanò, Tiziana; Meo, Paolo D’Onorio De; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

doi:10.1093/nar/gkj105

Cited by 271 publications

(173 citation statements)

References 29 publications

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“…Fig. S2 and Supporting Information) and deposited in the Protein Model Database [Castrignano et al, 2006] (PMDB id: PM0077187). The mutant amino acid substitution forms of PINK1 found in humans were taking from Deas and colleagues [2009] and mutation numbering system is based on codon 11 corresponding to the ATG translation initiation codon in the reference sequence.…”

Section: Methodsmentioning

confidence: 99%

“…We used as substrate a fragment of CaV1.2 (crystallized with Calmodulin, pdb ID: 2be6F) that includes the amino acid phosphorylated by CaMKII (T1603) [Wang et al, 2009]. The predicted structure for enzyme-substrate complexes for PINK1-CaV1.2 and CaMKIICaV1.2 were deposited in Protein Model Database [Castrignano et al, 2006] (PMDB ids: PM0076737 and PM0076739, respectively).…”

Section: Methodsmentioning

confidence: 99%

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Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

et al. 2011

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Parkinson disease (PD) is the second most common neurodegenerative disorder and is characterized by the loss of dopaminergic neurons in the substantia nigra. Mutations in PINK1 were shown to cause recessive familial PD, and today are proposed to be associated with the disease via mitochondrial dysfunction and oxidative damage. The PINK1 gene comprises eight exons, which encode a ubiquitously expressed 581 amino acid protein that contains an N-terminal mitochondrial targeting domain and a serine/threonine protein kinase. To better understand the relationship between PINK1 and PD we have first analyzed the evolutionary history of the gene showing its late emergence in evolution. In addition, we have modeled the three-dimensional structure of PINK1 and found some evidences that help to explain the effect of some PD-related mutations in this protein's function.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

et al. 2011

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show abstract

“…The target and template Density Optimization Potential Energy (DOPE) profiles were plotted using gnuplot (http:// www.gnuplot.info/), and Modeller SuperPose command was used to superimpose the 3D structures of template and target [16]. The developed 3D model of L. interrogans MurD was submitted to Protein Model Data Base (PMDB) [30], which collects 3D models obtained by structure prediction methods.…”

Section: Evaluation Of Model Qualitymentioning

confidence: 99%

Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase

2010

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The life-threatening infections caused by Leptospira serovars remain a global challenge since long time. Prevention of infection by controlling environmental factors being difficult to practice in developing countries, there is a need for designing potent anti-leptospirosis drugs. ATP-dependent MurD involved in biosynthesis of peptidoglycan was identified as common drug target among pathogenic Leptospira serovars through subtractive genomic approach. Peptidoglycan biosynthesis pathway being unique to bacteria and absent in host represents promising target for antimicrobial drug discovery. Thus, MurD 3D models were generated using crystal structures of 1EEH and 2JFF as templates in Modeller9v7. Structural refinement and energy minimization of the model was carried out in Maestro 9.0 applying OPLS-AA 2001 force field and was evaluated through Procheck, ProSA, PROQ, and Profile 3D. The active site residues were confirmed from the models in complex with substrate and inhibitor. Four published MurD inhibitors (two phosphinics, one sulfonamide, and one benzene 1,3-dicarbixylic acid derivative) were queried against more than one million entries of Ligand.Info Meta-Database to generate in-house library of 1,496 MurD inhibitor analogs. Our approach of virtual screening of the best-ranked compounds with pharmacokinetics property prediction has provided 17 novel MurD inhibitors for developing anti-leptospirosis drug targeting peptidoglycan biosynthesis pathway.

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“…The energy minimization was performed by using Swiss-PdbViewer (DeepView v4.1) and best model was selected. The PDB files thus generated were submitted to Protein Model Database (PMDB) and were used for further analysis [8].…”

Section: Homology Modellingmentioning

confidence: 99%

In Silico Analysis of Bacterial Functional Amyloids and their Interactions

Mehta¹

2018

IJRASET

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Amyloid proteins have been known to be responsible for many neurodegenerative diseases of mammals including humans. Histopathologically, amyloid fibres are known to be formed due to mis-folds, mutations and other induction events concerned with these proteins in the patients. Once formed, these amyloid proteins have been well reported to undergo nucleation and form fibrous projections that result in cell-death. In living system (microorganisms and higher organisms alike), similar functional amyloid proteins are known to be produced with similar nucleation process. In this report the homologous proteins were created for functional amyloids from Escherichia coli, Bacillus thuringiensis, Bacillus atropheus, Streptococcus pyogenes and Dinoroseobacter shibae. Using the Z-dock server, analysed their interaction with each other. This report will help in understanding the self-folding and nucleation process of the functional amyloids in bacteria and further correlate the functional amyloids of bacteria with pathological amyloids in mammals.

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The PMDB Protein Model Database

Cited by 271 publications

References 29 publications

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase

In Silico Analysis of Bacterial Functional Amyloids and their Interactions

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