The Protein Data Bank (PDB) & PDB Files

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The Protein Data Bank (PDB) & PDB Files Lesson Date: 09/01/04 – W Created by: Angela M. Amoia 08/20/04

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The Protein Data Bank (PDB) & PDB Files. Lesson Date: 09/01/04 – W Created by: Angela M. Amoia 08/20/04. Lesson Objectives. Recall what the PDB is and what is stores Recall what a PDB file is and what its contents stand for - PowerPoint PPT Presentation

Transcript of The Protein Data Bank (PDB) & PDB Files

  • The Protein Data Bank (PDB) & PDB FilesLesson Date: 09/01/04 WCreated by: Angela M. Amoia 08/20/04

  • Lesson ObjectivesRecall what the PDB is and what is storesRecall what a PDB file is and what its contents stand forSummarize two (2) ways to obtain PDB files associated with an articleSummarize how to find articles associated with a PDB file

  • Protein Data Bank (PDB)Single World Wide databaseStores atomic coordinates of protein & nucleic acid structures knownCoordinates determined by:X-Ray Crystallography NMRAssigned PDB ID or accession number4 characters; ex. 1ANG

  • PDB File (.pdb)Text file, viewed/modified in editor (TextPad)a.k.a. structure fileContains position of every atom in the file as well as some information about the structureHolds all the information needed to reconstruct a 3D model of a molecule view in RASMOL or DeepViewAt first, contents are intimidating! But they are actually quite simple documents!

  • Contents of PDB fileGeneral information about the molecule: name, ligands, sequence, references to journal articles, etc.

  • Contents of PDB fileInformation about each atom in the structure: arranged in sequence- first amino acid first, last amino acid last

  • How can I obtain PDB files associated with an article?

    Link from PubMed article to associated structures in PDB

    Directly from PDB using the PDB accession number acquired from a paper

  • If I already have a structure in mind, how can I find articles associated with it?

    Use the PDB search engine and link from the PDB to PubMed

  • Shall we


Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description ... - BIUofranservices.biu.ac.il/site/services/epitope/pdf/PDB... · 2014. 10. 14. · PDB File Format

Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description ... - BIUofranservices.biu.ac.il/site/services/epitope/pdf/PDB... · 2014. 10. 14. · PDB File Format

From: Protein Data Bank PDB ID: 1B0E Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C.,

From: Protein Data Bank PDB ID: 1B0E Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C.,

FUNDING Knowing the 3D structure of RCSB PDB SERVICES AT A …€¦ · Protein Data Bank organization, within which the RCSB PDB is responsible for US PDB operations and serves as

FUNDING Knowing the 3D structure of RCSB PDB SERVICES AT A …€¦ · Protein Data Bank organization, within which the RCSB PDB is responsible for US PDB operations and serves as

PDB-Protein Data Bank SCOP –Protein structure classification CATH –Protein structure classification genTHREADER–3D structure prediction Swiss-Model–3D.

PDB-Protein Data Bank SCOP –Protein structure classification CATH –Protein structure classification genTHREADER–3D structure prediction Swiss-Model–3D.

Staphylococcal bio lm-forming protein has a contiguous rod-like ... - PNAS · (21) in the Protein Data Bank (PDB; with low ∼15% sequence identity to SasG G5 domains), the E segments

Staphylococcal bio lm-forming protein has a contiguous rod-like ... - PNAS · (21) in the Protein Data Bank (PDB; with low ∼15% sequence identity to SasG G5 domains), the E segments

RESEARCH Open Access Structure based … this work, we have constructed 18 sets of same protein-RNA complexes belonging to different organisms from Protein Data Bank (PDB). The similarities

RESEARCH Open Access Structure based … this work, we have constructed 18 sets of same protein-RNA complexes belonging to different organisms from Protein Data Bank (PDB). The similarities

SODIUM-POTASSIUM PUMPcbm.msoe.edu/.../documents/sodiumPotassiumPump.pdfRCSB Protein Data Bank The Protein Data Bank (PDB) is the single worldwide repository for the processing and

SODIUM-POTASSIUM PUMPcbm.msoe.edu/.../documents/sodiumPotassiumPump.pdfRCSB Protein Data Bank The Protein Data Bank (PDB) is the single worldwide repository for the processing and

Pymol–!Tutorial! - bioinformatica.uab.esbioinformatica.uab.es/base/documents\bioinformaticsintranet... · Pymol–!Tutorial!! Go!to!!is!the!Protein!Data!Bank!(PDB)!=!adatabasefor!protein!structures.!!!!!

Pymol–!Tutorial! - bioinformatica.uab.esbioinformatica.uab.es/base/documents\bioinformaticsintranet... · Pymol–!Tutorial!! Go!to!!is!the!Protein!Data!Bank!(PDB)!=!adatabasefor!protein!structures.!!!!!

The Protein Data Bank in Europe (PDBe): bringing structure ... · The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions

The Protein Data Bank in Europe (PDBe): bringing structure ... · The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions

Bridging the Information Gap: Computational Tools for ......NMR, electron cryomicroscopy and modeling, the current structural database, the Protein Data Bank (PDB),1 which has greater

Bridging the Information Gap: Computational Tools for ......NMR, electron cryomicroscopy and modeling, the current structural database, the Protein Data Bank (PDB),1 which has greater

Acaaddemmiicc Sccii ennccess - innovareacademics.in · WHO declares that Indonesia has become the fourth country that has ... complexes available in Protein Data Bank (PDB) ().

Acaaddemmiicc Sccii ennccess - innovareacademics.in · WHO declares that Indonesia has become the fourth country that has ... complexes available in Protein Data Bank (PDB) ().

1 1.1. Introduction to Protein Data Bank Formatiruczins/teaching/260.655/links/pdbformat.pdf · 1 1.1. Introduction to Protein Data Bank Format Protein Data Bank (PDB) format is a

1 1.1. Introduction to Protein Data Bank Formatiruczins/teaching/260.655/links/pdbformat.pdf · 1 1.1. Introduction to Protein Data Bank Format Protein Data Bank (PDB) format is a

DNA Motif and protein domain discovery Presented by: Deeter Neumann Peter St. Andre PDB; zinc finger 224 PDB; human enhancer binding protein.

DNA Motif and protein domain discovery Presented by: Deeter Neumann Peter St. Andre PDB; zinc finger 224 PDB; human enhancer binding protein.

Protein data bank (PDB) : 46818 structures (oct 2007) SCOP (Structural Classification Of Proteins): 971 folds (major structural similarity) 1586 super-families.

Protein data bank (PDB) : 46818 structures (oct 2007) SCOP (Structural Classification Of Proteins): 971 folds (major structural similarity) 1586 super-families.

3D Protein Structure Visualization3D Protein Structure Search Search for 3D protein structure files obtained from the Protein Data Bank (PDB). Influenza protein(s) are associated with

3D Protein Structure Visualization3D Protein Structure Search Search for 3D protein structure files obtained from the Protein Data Bank (PDB). Influenza protein(s) are associated with

How many protein folds are there › forschung › bm › lehre › ...Typical numbers 105 structures in protein data bank (PDB) •much redundancy 1 ½ × 105 chains in PDB •even

How many protein folds are there › forschung › bm › lehre › ...Typical numbers 105 structures in protein data bank (PDB) •much redundancy 1 ½ × 105 chains in PDB •even

PDBe TUTORIAL PDBeFold (SSM: Secondary Structure …...Examination of a protein structure for similarity with the whole Protein Data Bank (PDB) archive or SCOP. Best C -alignment of

PDBe TUTORIAL PDBeFold (SSM: Secondary Structure …...Examination of a protein structure for similarity with the whole Protein Data Bank (PDB) archive or SCOP. Best C -alignment of

tein Compared toHuman and Mouse PrionProteins · prion protein (1AG2.pdb) was released into the PDB bank in 1997 and last modified in 2009 [Riek et al. 1996]. Rabbits, dogs and horses

tein Compared toHuman and Mouse PrionProteins · prion protein (1AG2.pdb) was released into the PDB bank in 1997 and last modified in 2009 [Riek et al. 1996]. Rabbits, dogs and horses

Structure Article - CORE · we attempt to answer this question, using the Protein Data Bank (PDB) to assess the useful-ness of inferred functional protein linkages from the Prolinks

Structure Article - CORE · we attempt to answer this question, using the Protein Data Bank (PDB) to assess the useful-ness of inferred functional protein linkages from the Prolinks

PROTEOMICS 3D Structure Prediction. Contents Protein 3D structure. –Basics –PDB –Prediction approaches Protein classification.

PROTEOMICS 3D Structure Prediction. Contents Protein 3D structure. –Basics –PDB –Prediction approaches Protein classification.