Structure Alignment

1
Structure Alignment Structure Similarity of
Proteins

• Introduction Overview

2
Outline

• From Sequence to Structure
• Protein Structure Alignment
• Protein Structure Similarity
• Framework For What
• What Can We Do
• Related Papers

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From Sequence to Structure

• Protein sequence amino acid
• Sequence alignment (local, global)
• Smith-Waterman, BLAST
• Pairwise, Multiple
• Sequence similarity
• Monte Carlo Experiment
• E-value
• Z-value
• P-value
• Bit score
• Sequence clustering

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Is it also useful in protein structure?

• Structure Alignment
• Structure Similarity
• Structural Motif
• Structure Clustering
• Structure Classification

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Sequence vs. 3D Structure

• Same Different
• Description string position coordinate
• Similarity amino acid string atom coordinate
• Alignment string atom position
• Representation subsequence substructure

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Protein Structure Alignment - 1

• Problem Definition
• Given two point sequences P and Q in
  3-dimensions, try to identify which positions or
  subpositions are similar in two protein 3D
  structures

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Example Structure Alignment - 1
Graph Matching
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Example Structure Alignment - 2
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Protein Structure Alignment - 2

• Methods
• Dynamic programming
• Mote Carlo
• 3D clustering
• Graph matching
• Combinatorial Extension (CE)
• Compound Likeness (CL)

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Protein Structure Similarity - 1

• Problem Definition
• Given a protein structure, find proteins in the
  database that have similar substructures

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Protein Structure Similarity - 2

• Measurement (Score)
• Coordinate Root-Mean-Square-Deviation (RMSDC)
• Distance Root-Mean-Square-Deviation (RMSDD)
• Unit-vector Root Mean Square (URMS)

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Framework 1
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Framework 2
Pairwise Comparison
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What Can We Do

• Goal Clustering
• What is our Features
• Atom position
• Substructure
• What kind of Tool do we need
• Alignment
• Similarity Function
• Methods for Feature Extraction
• Thinking

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Related Papers - 1

• Protein structure alignment by incremental
  combinatorial extension (CE) of the optimal path,
  Protein Eng. 1998 Sep11(9)739-47., Shindyalov
  IN, Bourne PE.
• A new algorithm for the alignment of multiple
  protein structures using Monte Carlo
  optimization, Pac Symp Biocomput. 2001275-86.,
  Guda C, Scheeff ED, Bourne PE, Shindyalov IN.
• Protein Structure Alignment Using Dynamic
  Programming and Iterative Improvement, IEICE
  TRANS. INF. SYST., VOL. E78-D, NO. 0 1996,
  Tatsuya AKUTSU

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Related Papers - 2

• Large-Scale Comparison of Protein Sequence
  Alignment Algorithms With Structure Alignments,
  J. Michael Sauder, Jonathan W. Arthur, Roland L.
  Dunbrack
• Regression Analysis of Multiple Protein
  Structures, Journal of Computational Biology,
  Thomas D. Wu, Trevor Hastie, Scott C. Schmidler,
  Douglas L. Brutlag
• Fast Substructure Searching Using the
  Conformational Likeness Method, Proceedings of
  the International Summer School on
  Crystallographic Computing Ed. P.E.Bourne
  K.Watenpaugh, 1996

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Related Paper - 3

• 3-D Homology of Proteins by Comformational
  Likeness, Proteins 1997, Submitted, M.P.
  Ponomarenko, I.N.Shindyalov P.E.BourneM.P.
  Ponomorenko, I.N. Shindyalov N. Kolchanov and
  P.E. Bourne
• Structure Comparison and Structure Patterns,
  Ingvar Eidhammer, Inge Jonassen, William R.
  Taylor
• Fast Detection of Common Geometric Substructure
  in Proteins, Journal of Computational Biology, L.
  Paul Chew Computer Science Department, Cornell
  University, Ithaca, NY