Conformation-independent structural comparison of macromolecules with ProSMART

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods.

[1]  Jay Painter,et al.  Electronic Reprint Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion , 2005 .

[2]  F. Cohen,et al.  A surface of minimum area metric for the structural comparison of proteins. , 1996, Journal of molecular biology.

[3]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[4]  M. Michael Gromiha,et al.  CUPSAT: prediction of protein stability upon point mutations , 2006, Nucleic Acids Res..

[5]  C. Chothia One thousand families for the molecular biologist , 1992, Nature.

[6]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[7]  David Sankoff,et al.  Comparison of musical sequences , 1990, Comput. Humanit..

[8]  Dimitri P. Bertsekas,et al.  Dynamic Programming and Optimal Control, Two Volume Set , 1995 .

[9]  J. Szustakowski,et al.  Protein structure alignment using a genetic algorithm , 2000, Proteins.

[10]  Roldan Pozo,et al.  Template Numerical Toolkit for Linear Algebra: High Performance Programming With C++ and the Standard Template Library , 1997, Int. J. High Perform. Comput. Appl..

[11]  Leszek Rychlewski,et al.  Fold-recognition detects an error in the Protein Data Bank , 2002, Bioinform..

[12]  Bo Li,et al.  Protein structure alignment based on internal coordinates , 2010, Interdisciplinary Sciences: Computational Life Sciences.

[13]  Lenore Cowen,et al.  Matt: Local Flexibility Aids Protein Multiple Structure Alignment , 2008, PLoS Comput. Biol..

[14]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[15]  Peter Briggs,et al.  A graphical user interface to the CCP4 program suite. , 2003, Acta crystallographica. Section D, Biological crystallography.

[16]  Ruth Nussinov,et al.  MASS: multiple structural alignment by secondary structures , 2003, ISMB.

[17]  M. Levitt,et al.  Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core , 1993, Current Biology.

[18]  J. Challis A procedure for determining rigid body transformation parameters. , 1995, Journal of biomechanics.

[19]  Jeffrey Skolnick,et al.  Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score , 2008, BMC Bioinformatics.

[20]  W. Kabsch A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .

[21]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[22]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[23]  S D O'Hearn,et al.  MolCom: a method to compare protein molecules based on 3-D structural and chemical similarity. , 2003, Protein engineering.

[24]  Chih-Hung Chang,et al.  Protein structural similarity search by Ramachandran codes , 2007, BMC Bioinformatics.

[25]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[26]  A. McCoy,et al.  SCEDS: protein fragments for molecular replacement in Phaser , 2013, Acta crystallographica. Section D, Biological crystallography.

[27]  H. Wolfson,et al.  Flexible protein alignment and hinge detection , 2002, Proteins.

[28]  Zhiping Weng,et al.  FAST: A novel protein structure alignment algorithm , 2004, Proteins.

[29]  A. D. McLachlan,et al.  Rapid comparison of protein structures , 1982 .

[30]  Randy J. Read,et al.  Advancing Methods for Biomolecular Crystallography , 2013 .

[31]  Fei Long,et al.  Low-resolution refinement tools in REFMAC5 , 2012, Acta crystallographica. Section D, Biological crystallography.

[32]  H. Berendsen,et al.  Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme , 1998, Proteins.

[33]  R. Cattell,et al.  The Procrustes Program: Producing direct rotation to test a hypothesized factor structure. , 2007 .

[34]  John C. Gower,et al.  Procrustes methods , 2010 .

[35]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[36]  Osvaldo Olmea,et al.  MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison , 2002, Protein science : a publication of the Protein Society.

[37]  BMC Bioinformatics , 2005 .

[38]  Gert Vriend,et al.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries , 2009, Acta crystallographica. Section D, Biological crystallography.

[39]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[40]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[41]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[42]  P E Bourne,et al.  The Protein Data Bank. , 2002, Nucleic acids research.

[43]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[44]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[45]  A. Konagurthu,et al.  MUSTANG: A multiple structural alignment algorithm , 2006, Proteins.

[46]  G M Crippen,et al.  Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. , 1994, Journal of molecular biology.

[47]  G. Kleywegt,et al.  Detecting folding motifs and similarities in protein structures. , 1997, Methods in enzymology.

[48]  Jon M. Kleinberg,et al.  Fast Detection of Common Geometric Substructure in Proteins , 1999, J. Comput. Biol..

[49]  Adam Godzik,et al.  Using an alignment of fragment strings for comparing protein structures , 2007, Bioinform..

[50]  Kian-Lee Tan,et al.  Matalign: Precise Protein Structure Comparison by Matrix Alignment , 2006, J. Bioinform. Comput. Biol..

[51]  J. Jung,et al.  Protein structure alignment using environmental profiles. , 2000, Protein engineering.

[52]  Anuj Srivastava,et al.  Statistical Shape Analysis , 2014, Computer Vision, A Reference Guide.

[53]  N. Go,et al.  Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. , 1992, Journal of molecular biology.

[54]  K. Nishikawa,et al.  Protein structure comparison using the Markov transition model of evolution , 2000, Proteins.

[55]  L. R. Rabiner,et al.  A comparative study of several dynamic time-warping algorithms for connected-word recognition , 1981, The Bell System Technical Journal.

[56]  Geoffrey Chang,et al.  Retraction of "Structure of MsbA from Vibrio cholera: a multidrug resistance ABC transporter homolog in a closed conformation" [J. Mol. Biol. (2003) 330 419-430]. , 2007, Journal of molecular biology.

[57]  J F Gibrat,et al.  Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.

[58]  A. Vagin,et al.  Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps. , 2001, Acta crystallographica. Section D, Biological crystallography.

[59]  S. McNicholas,et al.  Presenting your structures: the CCP4mg molecular-graphics software , 2011, Acta crystallographica. Section D, Biological crystallography.

[60]  T. Schneider,et al.  Domain identification by iterative analysis of error-scaled difference distance matrices. , 2004, Acta crystallographica. Section D, Biological crystallography.

[61]  K Henrick,et al.  Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. , 2004, Acta crystallographica. Section D, Biological crystallography.

[62]  Roberto Mosca,et al.  Alignment of protein structures in the presence of domain motions , 2008, BMC Bioinformatics.

[63]  Snigdhansu Chatterjee,et al.  Procrustes Problems , 2005, Technometrics.