The RCSB Protein Data Bank: redesigned web site and web services

Rose, Peter W.; Beran, Bojan; Bi, Chunxiao; Bluhm, Wolfgang F.; Dimitropoulos, Dimitris; Goodsell, David S.; Prlić, Andreas; Quesada, Martha; Quinn, Gregory B.; Westbrook, John D.; Young, Jasmine; Yukich, Benjamin T.; Zardecki, Christine; Berman, Helen M.; Bourne, Philip E.

doi:10.1093/nar/gkq1021

Cited by 566 publications

(457 citation statements)

References 32 publications

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“…The overall procedure of the structure set preparation is shown in Supporting Information Figure S6. A list of non-redundant 21,744 protein chains was obtained using the first element of each cluster in the clustering analysis of all protein chains in the PDB 28 by blastclust with 30% sequence identity (http://www.rcsb.org/pdb/statistics/clusterStatistics. do, as of March 2014).…”

Section: Random Local Structure Setmentioning

confidence: 99%

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Lee

2016

Protein Science

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Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of GLoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.

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Section: Random Local Structure Setmentioning

confidence: 99%

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Lee

2016

Protein Science

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“…There are number of CDK2 electronic structures available in protein databank [17]. The selection of 2BHH is due to presence of natural inhibitor located in one of the main active sties.…”

Section: Resultsmentioning

confidence: 99%

“…as a natural inhibitor [17]. The selected enzyme structure was prepared in such a way that it has no ambiguities in the form of missing atoms or amino acids.…”

Section: (2e3s)-3-hydroxy-5'-[(4-hydroxypiperidin-1-yl) Sulfonyl]-3-mentioning

confidence: 99%

Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme

Ganatra¹

2012

JCSB

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The knowledge of the molecular basis of carcinogenesis has helped to discover new, less toxic chemotherapy agents. At present, considerable attention has been focused on identifying the molecular level interactions of naturally occurring Terpene based substances, capable of inhibiting target enzymes. CDKs enzymes are known as cell regulators in eukaryotic cell cycle. In finding new anti-cancer agents, CDKs are used as target enzymes, particular among them are CDK2 enzymes.Computer based Chem-office and Autodock molecular modeling tools used to understand the ways with which Terpene based natural products interacts with Cyclin-dependent kinase 2 (CDK2). Using in-silico techniques, the binding energy between ligands and receptor enzyme are calculated in the form of ∆G in Kcal.mol -1 . The reported binding energies for series of molecules are ranging from -7.96 to -16.62 Kcal.mol -1 . The negative docking energies and a few hydrogen bonds between ligand and receptor enzyme support the affinity of Terpene based compounds with selected enzyme. Number of hydroxyl groups present in ligand enhances the interaction strength and stability of complex. The finding confirms the affinity of Terpene based natural products as CDK2 inhibitor. Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 EnzymeSunil H Ganatra* and Amita S Suchak Department of Chemistry, Institute of Science, Civil Lines, India Citation: Ganatra SH, Suchak AS (2012) Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme. J Comput Sci Syst Biol 5: 068-073.

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“…The DLC1 GAP domain (Protein Data Bank (PDB) ID: 3KUQ (22,23)) was used as the receptor and the RasGAP SH3 domain (PDB ID: 2J05 (24)) as the ligand. The receptor and ligand binding sites were not imposed, and no additional constraint was applied during the docking.…”

Section: Methodsmentioning

confidence: 99%

A WXW Motif Is Required for the Anticancer Activity of the TAT-RasGAP317–326 Peptide

Barras

Chevalier

Zoete

et al. 2014

Journal of Biological Chemistry

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Background: TAT-RasGAP 317-326 is a Ras GTPase-activating protein (RasGAP)-derived peptide that requires deleted in liver cancer-1 (DLC1) for its antimetastatic activities. Results: A WXW motif within TAT-RasGAP 317-326 mediates RasGAP-DLC1 interaction. Conclusion:The tryptophan residues of TAT-RasGAP 317-326 are crucial for its activity Significance: The WXW motif could be used to design anticancer small molecules bearing TAT-RasGAP 317-326 activities.

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The RCSB Protein Data Bank: redesigned web site and web services

Cited by 566 publications

References 32 publications

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme

A WXW Motif Is Required for the Anticancer Activity of the TAT-RasGAP317–326 Peptide

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