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Functional Annotation of Uncharacterized proteins in PDB

Functional Annotation of Uncharacterized proteins in PDB. Presented by : Swagata Naha Das Guided by : Dr Shuchismita Dutta. Process O verview. 3 Approaches :. RCSB Sequence/3D Similarity Literatures 10 Steps Method. RCSB Sequence Similarity/3D Alignment. Sequence Similarity

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Functional Annotation of Uncharacterized proteins in PDB

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  1. Functional Annotation of Uncharacterized proteins in PDB Presented by :Swagata Naha Das Guided by : Dr ShuchismitaDutta

  2. Process Overview 3 Approaches: • RCSB Sequence/3D Similarity • Literatures • 10 Steps Method

  3. RCSB Sequence Similarity/3DAlignment • Sequence Similarity • 100% Exact Match • 30% Neighbor Match • 3D Similarity • lowest p-value, %Id, Cov1, Cov2 • Ligand binding sites • conserved residues

  4. 10 Steps Approach • Based on Percentage Identity scale • >80 % Blast • 50 – 80 % PIRSF, COGs • < 50 % str neighbors SCOP, VAST • <30% Analysis of Seq/Str motifs PDBsum, LPC/CSU Figure: Percent Identity Scale Citation: MazumderR ,Vasudevan S(2008)

  5. Few Examples Figure: RCSB PDB and 10 steps

  6. Few Examples Figure: literature

  7. Examples of Missed entries

  8. Conclusion: By Comparison Functions! • RCSB Sequence/3D Similarity • 10 Steps Method • Literatures

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