BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

273 related articles for article (PubMed ID: 25540181)

  • 1. The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
    Westbrook JD; Shao C; Feng Z; Zhuravleva M; Velankar S; Young J
    Bioinformatics; 2015 Apr; 31(8):1274-8. PubMed ID: 25540181
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
    Burley SK; Berman HM; Kleywegt GJ; Markley JL; Nakamura H; Velankar S
    Methods Mol Biol; 2017; 1607():627-641. PubMed ID: 28573592
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Small molecule annotation for the Protein Data Bank.
    Sen S; Young J; Berrisford JM; Chen M; Conroy MJ; Dutta S; Di Costanzo L; Gao G; Ghosh S; Hudson BP; Igarashi R; Kengaku Y; Liang Y; Peisach E; Persikova I; Mukhopadhyay A; Narayanan BC; Sahni G; Sato J; Sekharan M; Shao C; Tan L; Zhuravleva MA
    Database (Oxford); 2014; 2014():bau116. PubMed ID: 25425036
    [TBL] [Abstract][Full Text] [Related]  

  • 4. The Protein Data Bank Archive.
    Velankar S; Burley SK; Kurisu G; Hoch JC; Markley JL
    Methods Mol Biol; 2021; 2305():3-21. PubMed ID: 33950382
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Remediation of the protein data bank archive.
    Henrick K; Feng Z; Bluhm WF; Dimitropoulos D; Doreleijers JF; Dutta S; Flippen-Anderson JL; Ionides J; Kamada C; Krissinel E; Lawson CL; Markley JL; Nakamura H; Newman R; Shimizu Y; Swaminathan J; Velankar S; Ory J; Ulrich EL; Vranken W; Westbrook J; Yamashita R; Yang H; Young J; Yousufuddin M; Berman HM
    Nucleic Acids Res; 2008 Jan; 36(Database issue):D426-33. PubMed ID: 18073189
    [TBL] [Abstract][Full Text] [Related]  

  • 6. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
    Berman H; Henrick K; Nakamura H; Markley JL
    Nucleic Acids Res; 2007 Jan; 35(Database issue):D301-3. PubMed ID: 17142228
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Using MSDchem to search the PDB ligand dictionary.
    Dimitropoulos D; Ionides J; Henrick K
    Curr Protoc Bioinformatics; 2006 Oct; Chapter 14():14.3.1-14.3.21. PubMed ID: 18428761
    [TBL] [Abstract][Full Text] [Related]  

  • 8. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
    Burley SK; Bhikadiya C; Bi C; Bittrich S; Chao H; Chen L; Craig PA; Crichlow GV; Dalenberg K; Duarte JM; Dutta S; Fayazi M; Feng Z; Flatt JW; Ganesan SJ; Ghosh S; Goodsell DS; Green RK; Guranovic V; Henry J; Hudson BP; Khokhriakov I; Lawson CL; Liang Y; Lowe R; Peisach E; Persikova I; Piehl DW; Rose Y; Sali A; Segura J; Sekharan M; Shao C; Vallat B; Voigt M; Webb B; Westbrook JD; Whetstone S; Young JY; Zalevsky A; Zardecki C
    Protein Sci; 2022 Dec; 31(12):e4482. PubMed ID: 36281733
    [TBL] [Abstract][Full Text] [Related]  

  • 9. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.
    Burley SK; Berman HM; Christie C; Duarte JM; Feng Z; Westbrook J; Young J; Zardecki C
    Protein Sci; 2018 Jan; 27(1):316-330. PubMed ID: 29067736
    [TBL] [Abstract][Full Text] [Related]  

  • 10. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.
    Sehnal D; Svobodová Vařeková R; Pravda L; Ionescu CM; Geidl S; Horský V; Jaiswal D; Wimmerová M; Koča J
    Nucleic Acids Res; 2015 Jan; 43(Database issue):D369-75. PubMed ID: 25392418
    [TBL] [Abstract][Full Text] [Related]  

  • 11. The Protein Data Bank: unifying the archive.
    Westbrook J; Feng Z; Jain S; Bhat TN; Thanki N; Ravichandran V; Gilliland GL; Bluhm W; Weissig H; Greer DS; Bourne PE; Berman HM
    Nucleic Acids Res; 2002 Jan; 30(1):245-8. PubMed ID: 11752306
    [TBL] [Abstract][Full Text] [Related]  

  • 12. AutoDep: a web-based system for deposition and validation of macromolecular structural -information.
    Lin D; Manning NO; Jiang J; Abola EE; Stampf D; Prilusky J; Sussman JL
    Acta Crystallogr D Biol Crystallogr; 2000 Jul; 56(Pt 7):828-41. PubMed ID: 10930830
    [TBL] [Abstract][Full Text] [Related]  

  • 13. RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive.
    Rose Y; Duarte JM; Lowe R; Segura J; Bi C; Bhikadiya C; Chen L; Rose AS; Bittrich S; Burley SK; Westbrook JD
    J Mol Biol; 2021 May; 433(11):166704. PubMed ID: 33186584
    [TBL] [Abstract][Full Text] [Related]  

  • 14. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.
    Burley SK; Bhikadiya C; Bi C; Bittrich S; Chen L; Crichlow GV; Duarte JM; Dutta S; Fayazi M; Feng Z; Flatt JW; Ganesan SJ; Goodsell DS; Ghosh S; Kramer Green R; Guranovic V; Henry J; Hudson BP; Lawson CL; Liang Y; Lowe R; Peisach E; Persikova I; Piehl DW; Rose Y; Sali A; Segura J; Sekharan M; Shao C; Vallat B; Voigt M; Westbrook JD; Whetstone S; Young JY; Zardecki C
    Protein Sci; 2022 Jan; 31(1):187-208. PubMed ID: 34676613
    [TBL] [Abstract][Full Text] [Related]  

  • 15. PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.
    Choudhary P; Feng Z; Berrisford J; Chao H; Ikegawa Y; Peisach E; Piehl DW; Smith J; Tanweer A; Varadi M; Westbrook JD; Young JY; Patwardhan A; Morris KL; Hoch JC; Kurisu G; Velankar S; Burley SK
    Database (Oxford); 2024 May; 2024():. PubMed ID: 38803272
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.
    Prlic A; Kalro T; Bhattacharya R; Christie C; Burley SK; Rose PW
    Bioinformatics; 2016 Dec; 32(24):3833-3835. PubMed ID: 27551105
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Chemical annotation of small and peptide-like molecules at the Protein Data Bank.
    Young JY; Feng Z; Dimitropoulos D; Sala R; Westbrook J; Zhuravleva M; Shao C; Quesada M; Peisach E; Berman HM
    Database (Oxford); 2013; 2013():bat079. PubMed ID: 24291661
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Pre-calculated protein structure alignments at the RCSB PDB website.
    Prlic A; Bliven S; Rose PW; Bluhm WF; Bizon C; Godzik A; Bourne PE
    Bioinformatics; 2010 Dec; 26(23):2983-5. PubMed ID: 20937596
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Ligand Depot: a data warehouse for ligands bound to macromolecules.
    Feng Z; Chen L; Maddula H; Akcan O; Oughtred R; Berman HM; Westbrook J
    Bioinformatics; 2004 Sep; 20(13):2153-5. PubMed ID: 15059838
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
    Suzuki H; Kawabata T; Nakamura H
    Bioinformatics; 2016 Feb; 32(4):619-20. PubMed ID: 26508754
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 14.