Computational analysis of evolution and conservation in a protein superfamily.

[1]  S. Salzberg,et al.  Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. , 2003, Nucleic acids research.

[2]  Jimin Pei,et al.  PCMA: fast and accurate multiple sequence alignment based on profile consistency , 2003, Bioinform..

[3]  N. Grishin,et al.  COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. , 2003, Journal of molecular biology.

[4]  P. Gettins.  Serpin structure, mechanism, and function. , 2002, Chemical reviews.

[5]  Arthur M Lesk,et al.  Serpins in prokaryotes. , 2002, Molecular biology and evolution.

[6]  M. Madera,et al.  A comparison of profile hidden Markov model procedures for remote homology detection. , 2002, Nucleic acids research.

[7]  H. Ragg,et al.  Widespread occurrence of serpin genes with multiple reactive centre-containing exon cassettes in insects and nematodes. , 2002, Gene.

[8]  Martin Vingron,et al.  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing , 2002, Bioinform..

[9]  Sudhir Kumar,et al.  MEGA2: molecular evolutionary genetics analysis software , 2001, Bioinform..

[10]  J. Whisstock,et al.  The Serpins Are an Expanding Superfamily of Structurally Similar but Functionally Diverse Proteins , 2001, The Journal of Biological Chemistry.

[11]  W. Atchley,et al.  Phylogenetic analyses of amino acid variation in the serpin proteins. , 2001, Molecular biology and evolution.

[12]  A Tramontano,et al.  Structural conservation in single-domain proteins: implications for homology modeling. , 2001, Journal of structural biology.

[13]  W. Atchley,et al.  Vertebrate serpins: construction of a conflict-free phylogeny by combining exon-intron and diagnostic site analyses. , 2001, Molecular biology and evolution.

[14]  Martin Vingron,et al.  Limits of homology detection by pairwise sequence comparison , 2001, Bioinform..

[15]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[16]  L. Mirny,et al.  Evolutionary conservation of the folding nucleus. , 2000, Journal of molecular biology.

[17]  A M Lesk,et al.  Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function. , 2000, Genome research.

[18]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[19]  Wen-Hsiung Li,et al.  NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. , 2000, Molecular biology and evolution.

[20]  A. Lapedes,et al.  Timing the ancestor of the HIV-1 pandemic strains. , 2000, Science.

[21]  N. Goldman,et al.  Codon-substitution models for heterogeneous selection pressure at amino acid sites. , 2000, Genetics.

[22]  Liisa Holm,et al.  Sequence search algorithm assessment and testing toolkit (SAT) , 2000, Bioinform..

[23]  C Chothia,et al.  Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. , 2000, Journal of molecular biology.

[24]  J. Irving,et al.  Human ovalbumin serpin evolution: phylogenic analysis, gene organization, and identification of new PI8-related genes suggest that two interchromosomal and several intrachromosomal duplications generated the gene clusters at 18q21-q23 and 6p25. , 1999, Genomics.

[25]  D Eisenberg,et al.  Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. , 1999, Journal of molecular biology.

[26]  D. Haussler,et al.  Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.

[27]  S F Altschul,et al.  Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. , 1998, Trends in biochemical sciences.

[28]  Thomas L. Madden,et al.  Protein sequence similarity searches using patterns as seeds. , 1998, Nucleic acids research.

[29]  Chris Sander,et al.  Removing near-neighbour redundancy from large protein sequence collections , 1998, Bioinform..

[30]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[31]  G. Silverman,et al.  Cytoplasmic antiproteinase 2 (PI8) and bomapin (PI10) map to the serpin cluster at 18q21.3. , 1997, Genomics.

[32]  O. Gotoh.  Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. , 1996, Journal of molecular biology.

[33]  K. Strimmer,et al.  Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies , 1996 .

[34]  M. Wilkinson,et al.  Majority-rule reduced consensus trees and their use in bootstrapping. , 1996, Molecular biology and evolution.

[35]  A Rzhetsky,et al.  Interior-branch and bootstrap tests of phylogenetic trees. , 1995, Molecular biology and evolution.

[36]  M. Wilkinson.  Common Cladistic Information and its Consensus Representation: Reduced Adams and Reduced Cladistic Consensus Trees and Profiles , 1994 .

[37]  M. Nei,et al.  Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. , 1994, Molecular biology and evolution.

[38]  R. Carrell,et al.  Effects of mutations in the hinge region of serpins. , 1993, Biochemistry.

[39]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

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

[41]  Nicholas D. Hastie,et al.  Accelerated evolution in the reactive centre regions of serine protease inhibitors , 1987, Nature.

[42]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[43]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[44]  Fred R. McMorris,et al.  Consensusn-trees , 1981 .

[45]  J. Felsenstein.  Maximum-likelihood estimation of evolutionary trees from continuous characters. , 1973, American journal of human genetics.

[46]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[47]  T. T. Wu,et al.  AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY , 1970, The Journal of experimental medicine.

[48]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[49]  Peer Bork,et al.  Recent improvements to the SMART domain-based sequence annotation resource , 2002, Nucleic Acids Res..

[50]  Neil D. Rawlings,et al.  MEROPS: the protease database , 2002, Nucleic Acids Res..

[51]  Arthur M. Lesk,et al.  Introduction to bioinformatics , 2002 .

[52]  Olivier Poch,et al.  BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations , 2001, Nucleic Acids Res..

[53]  A. Halpern,et al.  Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. , 2000, Molecular biology and evolution.

[54]  M. Tristem.  Molecular Evolution — A Phylogenetic Approach. , 2000, Heredity.

[55]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[56]  W. Pearson.  Effective protein sequence comparison. , 1996, Methods in enzymology.

[57]  M. Nei,et al.  Phylogenetic analysis in molecular evolutionary genetics. , 1996, Annual review of genetics.

[58]  J. Thompson,et al.  Using CLUSTAL for multiple sequence alignments. , 1996, Methods in enzymology.