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exploring 3d molecular structures using ncbi tools

NCBI Structure Resources. Overview of Structural Informatics at NCBIHow 3D Macromolecular Structures are DeterminedIndexing Structural Data at NCBIFinding Homologous StructuresBy Sequence Similarity: BLASTBy Structure Similarity: VASTBy Conserved Function: RPS-BLAST and CDDFinding a Structural Template for a Query Protein.

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exploring 3d molecular structures using ncbi tools

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    1. Exploring 3D Molecular Structures Using NCBI Tools

    2. NCBI Structure Resources Overview of Structural Informatics at NCBI How 3D Macromolecular Structures are Determined Indexing Structural Data at NCBI Finding Homologous Structures By Sequence Similarity: BLAST By Structure Similarity: VAST By Conserved Function: RPS-BLAST and CDD Finding a Structural Template for a Query Protein

    3. The National Center for Biotechnology Information

    4. Structural Informatics

    5. Structural Informatics

    6. Structural Informatics at NCBI

    7. The Entrez System

    8. Solving Structures

    9. More About Resolution

    10. Solving Structures

    11. PDB

    12. PDB File: Header

    13. PDB File: Data

    14. From PDB to Entrez

    15. From Coordinates to Models

    16. Building the Structure Summary

    17. Indexing into MMDB

    18. Structure Indexing

    19. Creating Sequence Records

    20. Building the Structure Summary

    21. Building the Structure Summary

    22. Annotating Secondary Structure

    23. Creating 3D Domains

    24. Creating 3D Domains

    25. Building the Structure Summary

    26. Building the Structure Summary

    27. 3D Domain Indexing

    28. Conserved Domains

    29. Linking Sequence to Function

    30. Entrez Domains (CDD v2.00)

    31. CD-Search Output

    32. CD Summary

    33. Building the Structure Summary

    34. Building the Structure Summary

    35. Creating Entrez Links

    36. Links to CDs

    37. Finding Homologous Structures By sequence similarity: BLAST By structural similarity: VAST By conserved function: CD-Search

    38. BLAST: Sequence Neighbors

    39. BLink Neighbors

    40. Related Structures from BLASTp

    41. Related Structures

    42. VAST: Searching by Structure

    43. VAST: Structure Neighbors structure: 1RCBstructure: 1RCB

    44. VAST: Calculate fij structure: 1RCBstructure: 1RCB

    45. VAST: Calculate (rik, zik) structure: 1RCBstructure: 1RCB

    46. VAST: Create Comparison Graph

    47. VAST: Refinement

    48. VAST: Alignment of Sequence

    49. VAST: Scoring

    50. VAST: Summary

    51. Query by Chain vs 3D Domain

    52. VAST: Multiple Alignments

    53. nr-PDB Sets

    54. Submitting a PDB File to VAST

    55. Blocks in CD Alignments

    56. Curating CD Alignments

    57. Curated CD Summary

    58.

    59. CDART

    60. Finding a Structural Template

    61. BLOCKER: The Block Aligner

    62. BLAST/PSSM vs BLOCKER

    63. The NCBI Threader

    64. The Future More curated CDs: they keep coming… Pre-computed Related Structures for all sequences in Entrez Protein CD “children”: subfamilies of large CD records based on sequence and structure similarity Improved mapping of SNP data onto 3D structures Further linking of structural and genomic biology

    65. What comes next… Workshop I Working with Structures Workshop II Working with Alignments All exercises and other resources will remain on the course web pages info@ncbi.nlm.nih.gov NCBI Handbook, Ch. 3

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