Výsledky vyhledávání - "PDB, Protein Data Bank"

Akademický článek

PDB-REPRDB: a database of representative protein chains in PDB (Protein Data Bank).

Autor: Noguchi T; Parallel Application Laboratory, Tsukuba Research Center, Real World Computing Partnership, Japan. noguchi@trc.rwcp.or.jp, Onizuka K, Akiyama Y, Saito M

Publikováno v: Proceedings. International Conference on Intelligent Systems for Molecular Biology [Proc Int Conf Intell Syst Mol Biol] 1997; Vol. 5, pp. 214-7.

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PDB-REPRDB: a database of representative protein chains in PDB (Protein Data Bank)

Autor: T, Noguchi, K, Onizuka, Y, Akiyama, M, Saito

Publikováno v: Proceedings. International Conference on Intelligent Systems for Molecular Biology. 5

We propose a novel set of 'representative' protein chains in PDB, where not only sequential but also structural similarities are taken into account. Hobohm et al. have already proposed "PDB_SELECT", which eliminates redundant chains based solely on s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::e4218d9b9699a6ee7d8e97b419850b33
https://pubmed.ncbi.nlm.nih.gov/9322039

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Periodical

Protein Structure Similarity Clustering: Dynamic Treatment of PDB Structures Facilitates ClusteringThis research was supported by the Max-Planck-Gesellschaft, the Deutsche Forschungsgemeinschaft, and the Fonds der Chemischen Industrie. D.B.B. thanks the Max-Planck-Gesellschaft (sabbatical stay), the American Heart Association (GIA 0650014Z), and NIH (CA 62034 and RR016544-01) for support. B.D.C. acknowledges a UCARE fellowship. R.G.M. acknowledges support from the NIH (CA 91885). We thank Dr. Ingrid R. Vetter for useful discussions. PDB=protein data bank.

Autor: Charette, Bradley D., MacDonald, Richard G., Wetzel, Stefan, Berkowitz, David B., Waldmann, Herbert

Publikováno v: Angewandte Chemie; November 2006, Vol. 118 Issue: 46 p7930-7934, 5p

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Conference

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Periodical

Glycosylation of prions and its effects on protein conformation relevant to amino acid mutations11Abbreviations: PrP, prion protein; PrPC, normal cellular isoform of prion protein; PrPSc, pathogenic scrapie isoform of prion protein; mPrP, mouse PrP; mPrP (124-231), fragment of mPrP; mPrP (23-231), complete polypeptide of mature mPrP; hPrP, human PrP; MD, molecular dynamics; GlcNAc, N-acetyl-D-glucosamine; Fuc, fucose; NMR, nuclear magnetic resonance; PDB, protein data bank; PDB1ag2, the code number of the atom coordinates of the refined mean structure of mPrP (121-231), which has been deposited in the PDB; TSE, transmissible spongiform encephalopathy.

Autor: Wong, Nicky K.C, Renouf, David V, Lehmann, Sylvain, Hounsell, Elizabeth F

Publikováno v: Journal of Molecular Graphics and Modelling; 2000, Vol. 18 Issue: 2 p126-134, 9p

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Akademický článek

The Lack of a Centralized and Universal Tool for Input File Generation for Molecular Dynamics Simulations and the Development of such a Tool

Autor: Muhammad Taimoor Khan, Ayesha Ameen

Publikováno v: Bioscientific Review, Vol 1, Iss 1 (2019)

This study aims to design and develop a tool that can efficiently generate Molecular Dynamics (MD) simulation input files and systems for various simulation software such as NAMD, Amber and GROMACS collectively using a single platform. Molecular Dyna

Externí odkaz: https://doaj.org/article/747d275794454879936f10d6cd8263eb

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Discovery of novel selective PI3Kγ inhibitors through combining machine learning-based virtual screening with multiple protein structures and bio-evaluation

Autor: Yanfei Cai, Jingyu Zhu, Yun Chen, Jian Jin, Xinling Zhao, Kan Li, Lei Xu, Huazhong Li, Gang Huang

Publikováno v: Journal of Advanced Research
Journal of Advanced Research, Vol 36, Iss, Pp 1-13 (2022)

Graphical abstract
Highlights • Virtual screening based on machine learning with multiple proteins was developed. • Discovery of a novel PI3Kγ inhibitor integrating virtual screening and bio-assays. • JN-KI3 selective inhibit PI3Kγ enzym

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2cdbf7fb8f578b72a0c3242e69513c71
https://doi.org/10.1016/j.jare.2021.04.007

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D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1

Autor: Suchetana Gupta, Ditipriya Mallick, Kumarjeet Banerjee, Shrimon Mukherjee, Soumyadev Sarkar, Sonny TM Lee, Partha Basuchowdhuri, Siddhartha S Jana

Publikováno v: Computational and Structural Biotechnology Journal, Vol 20, Iss, Pp 766-778 (2022)
Computational and Structural Biotechnology Journal

Graphical abstract
The clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c77e75e84ff2110441d6e92dcaabf7e8
http://www.sciencedirect.com/science/article/pii/S2001037022000241

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