2018年Local Flexibility Aids Protein Multiple Structure Alignment局部柔度艾滋病蛋白质多结构比对-文档资料.ppt
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1、Inferring structural similarity from homology is hard at the SCOP superfamily/fold level,Profile HMMs,HMM is trained from Sequence Alignment of Known Structures,But: cannot capture pariwise long-range beta-sheet interactions!,HMMs cannot capture statistical preferences from residues close in space b
2、ut far, and a variable distance apart in seq.,Pectate Lyase C (Yoder et al. 1993),Look at Just Pairs or Generalize to Markov Random Fields,Only look at Pairs:,Generalize to Markov Random Fields Liu et al. 2009 Zhao et al. 2010 Menke et al. 2010 (This work),Bradley, Cowen, Menke, King, Berger, PNAS,
3、2001, 98:26, 14,819-14,824 ; Cowen, Bradley, Menke, King, Berger (2002), J Comp Biol, 9, 261-276,Lets look at what this would mean for propeller folds,Goal: capture HMM sequence information and pairwise information in beta-structural motifs at the same time!,SCOP (http:/scop.mrc-lmb.cam.ac.uk/scop,S
4、tructural Motifs Using Random Fields,SMURF,Structural Motifs Using Random Fields,Can we get the benefit of pairwise correlations without having to throw away all sequence info?,The template is learned from solved structures in the PDB,The template is learned from solved structures in the PDB: Aligne
5、d with Matt,Digression: Matt structural alignment program,Menke, Berger, Cowen, (PLOS Combio 2008) Specifically designed to align more distant homologs AFP chaining using dynamic programming with “translations and twists” (flexibility),The template is learned from solved structures in the PDB: Align
6、ed with Matt,Two beta tables are learned from amphapathic beta sheets that are not propellers from solved structures in the PDB.,Buried Residue,Exposed Residue,http:/bcb.cs.tufts.edu/propellers/si/,Two pairwise,Computing a Score,Sequences are scored by computing their best “threading” or “parse” aga
7、inst the template as a sum of HMM(score) + pairwise(score) No longer polynomial time (multi-dimensional dynamic programming) Tractable on propellers because paired beta-strands dont interleave too much,Lets look at what this would mean for propeller folds,Lets look at what this would mean for propel
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