Multiple Sequence Alignment.
暂无分享,去创建一个
[1] Simon Easteal,et al. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. , 2007, Molecular biology and evolution.
[2] R. Doolittle,et al. Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.
[3] Tu Minh Phuong,et al. Multiple alignment of protein sequences with repeats and rearrangements , 2006, Nucleic acids research.
[4] Jaap Heringa,et al. Global multiple‐sequence alignment with repeats , 2006, Proteins.
[5] Iain M. Wallace,et al. M-Coffee: combining multiple sequence alignment methods with T-Coffee , 2006, Nucleic acids research.
[6] Erik L. L. Sonnhammer,et al. Kalign – an accurate and fast multiple sequence alignment algorithm , 2005, BMC Bioinformatics.
[7] Yaoqi Zhou,et al. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. , 2005, Bioinformatics.
[8] Jaap Heringa,et al. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information , 2005, Nucleic Acids Res..
[9] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[10] Lode Wyns,et al. SABmark- a benchmark for sequence alignment that covers the entire known fold space , 2005, Bioinform..
[11] Chuong B. Do,et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.
[12] K. Katoh,et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.
[13] Kuang Lin,et al. A simple and fast secondary structure prediction method using hidden neural networks , 2005, Bioinform..
[14] G. Crooks,et al. A generalized affine gap model significantly improves protein sequence alignment accuracy , 2004, Proteins.
[15] W. Taylor. A flexible method to align large numbers of biological sequences , 2005, Journal of Molecular Evolution.
[16] P. Hogeweg,et al. The alignment of sets of sequences and the construction of phyletic trees: An integrated method , 2005, Journal of Molecular Evolution.
[17] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[18] Cédric Notredame,et al. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. , 2004, Journal of molecular biology.
[19] Burkhard Morgenstern,et al. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ , 2004, Nucleic Acids Res..
[20] A. Krogh,et al. A combined transmembrane topology and signal peptide prediction method. , 2004, Journal of molecular biology.
[21] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[22] Geoffrey J. Barton,et al. The Jalview Java alignment editor , 2004, Bioinform..
[23] Robert C. Edgar,et al. Local homology recognition and distance measures in linear time using compressed amino acid alphabets. , 2004, Nucleic acids research.
[24] Gajendra P. S. Raghava,et al. OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy , 2003, BMC Bioinformatics.
[25] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[26] Jaap Heringa,et al. Local Weighting Schemes for Protein Multiple Sequence Alignment , 2002, Comput. Chem..
[27] Melissa S. Cline,et al. Predicting reliable regions in protein sequence alignments , 2002, Bioinform..
[28] T L Blundell,et al. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.
[29] Christoph Gille,et al. STRAP: editor for STRuctural Alignments of Proteins , 2001, Bioinform..
[30] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[31] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[32] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[33] Jaap Heringa,et al. Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment , 1999, Comput. Chem..
[34] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[35] Olivier Poch,et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..
[36] A. Michie,et al. CINEMA--a novel colour INteractive editor for multiple alignments. , 1998, Gene.
[37] S F Altschul,et al. Generalized affine gap costs for protein sequence alignment , 1998, Proteins.
[38] Ian Holmes,et al. Dynamic programming alignment accuracy , 1998, RECOMB '98.
[39] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[40] Jens Stoye,et al. DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment , 1997, Comput. Appl. Biosci..
[41] J. Thompson,et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.
[42] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[43] Chris Sander,et al. Objectively judging the quality of a protein structure from a Ramachandran plot , 1997, Comput. Appl. Biosci..
[44] W R Taylor,et al. Three-dimensional domain duplication, swapping and stealing. , 1997, Current opinion in structural biology.
[45] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[46] D Eisenberg,et al. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. , 1997, Journal of molecular biology.
[47] J. Garnier,et al. Protein topology recognition from secondary structure sequences: application of the hidden Markov models to the alpha class proteins. , 1997, Journal of molecular biology.
[48] E S Huang,et al. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. , 1997, Journal of molecular biology.
[49] D. Eisenberg. Into the black of night , 1997, Nature Structural Biology.
[50] J. Skolnick,et al. MONSSTER: a method for folding globular proteins with a small number of distance restraints. , 1997, Journal of molecular biology.
[51] Terri K. Attwood,et al. Novel developments with the PRINTS protein fingerprint database , 1997, Nucleic Acids Res..
[52] 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.
[53] Manolo Gouy,et al. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny , 1996, Comput. Appl. Biosci..
[54] C. Sander,et al. The prediction of protein contacts from multiple sequence alignments. , 1996, Protein engineering.
[55] R. King,et al. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction , 1996, Protein science : a publication of the Protein Society.
[56] A. Dress,et al. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[57] W R Taylor,et al. Homology modelling by distance geometry. , 1996, Folding & design.
[58] F. Cohen,et al. Multiple sequence information for threading algorithms. , 1996, Journal of molecular biology.
[59] Y. Edwards,et al. Assessment of protein fold predictions from sequence information: the predicted alpha/beta doubly wound fold of the von Willebrand factor type A domain is similar to its crystal structure. , 1996, Journal of molecular biology.
[60] G. Barton,et al. Protein fold recognition by mapping predicted secondary structures. , 1996, Journal of molecular biology.
[61] M. Vásquez,et al. Modeling side-chain conformation. , 1996, Current opinion in structural biology.
[62] J Moult,et al. Genetic algorithms for protein structure prediction. , 1996, Current opinion in structural biology.
[63] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[64] D. Higgins,et al. SAGA: sequence alignment by genetic algorithm. , 1996, Nucleic acids research.
[65] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[66] Kevin Karplus,et al. A Flexible Motif Search Technique Based on Generalized Profiles , 1996, Comput. Chem..
[67] M C Peitsch,et al. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. , 1996, Biochemical Society transactions.
[68] D T Jones,et al. Protein fold recognition by sequence threading: tools and assessment techniques , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[69] William R. Taylor,et al. A non-local gap-penalty for profile alignment , 1996 .
[70] P. Argos,et al. SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.
[71] J. Gibrat,et al. GOR method for predicting protein secondary structure from amino acid sequence. , 1996, Methods in enzymology.
[72] S Subbiah,et al. How similar must a template protein be for homology modeling by side-chain packing methods? , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[73] Rolf Apweiler,et al. The SWISS-PROT protein sequence data bank and its new supplement TREMBL , 1996, Nucleic Acids Res..
[74] J. Moult,et al. Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms , 1995, Proteins.
[75] B Rost,et al. Progress of 1D protein structure prediction at last , 1995, Proteins.
[76] J M Thornton,et al. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing , 1995, Proteins.
[77] M Levitt,et al. Recognizing native folds by the arrangement of hydrophobic and polar residues. , 1995, Journal of molecular biology.
[78] Osamu Gotoh,et al. A weighting system and algorithm for aligning many phylogenetically related sequences , 1995, Comput. Appl. Biosci..
[79] A. Godzik,et al. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets , 1995, Protein science : a publication of the Protein Society.
[80] E. Shakhnovich,et al. Exhaustive enumeration of protein conformations using experimental restraints , 1995, Protein science : a publication of the Protein Society.
[81] M J Rooman,et al. Are database-derived potentials valid for scoring both forward and inverted protein folding? , 1995, Protein engineering.
[82] S. Sun,et al. A genetic algorithm that seeks native states of peptides and proteins. , 1995, Biophysical journal.
[83] K. Dill,et al. A simple protein folding algorithm using a binary code and secondary structure constraints. , 1995, Protein engineering.
[84] A V Finkelstein,et al. Accurate general method for lattice approximation of three‐dimensional structure of a chain molecule , 1995, Proteins.
[85] E I Shakhnovich,et al. Domains in folding of model proteins , 1995, Protein science : a publication of the Protein Society.
[86] G J Barton,et al. Protein secondary structure prediction. , 1995, Current opinion in structural biology.
[87] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[88] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[89] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[90] E I Shakhnovich,et al. A test of lattice protein folding algorithms. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[91] W R Taylor,et al. An investigation of conservation-biased gap-penalties for multiple protein sequence alignment. , 1995, Gene.
[92] M. Levitt,et al. The complexity and accuracy of discrete state models of protein structure. , 1995, Journal of molecular biology.
[93] David T. Jones,et al. Protein superfamilles and domain superfolds , 1994, Nature.
[94] L. Wyns,et al. The structures of rnase a complexed with 3′‐CMP and d(CpA): Active site conformation and conserved water molecules , 1994, Protein science : a publication of the Protein Society.
[95] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[96] D. Wigley,et al. The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. , 1994, Journal of molecular biology.
[97] M. Levitt,et al. Exploring conformational space with a simple lattice model for protein structure. , 1994, Journal of molecular biology.
[98] Timothy F. Havel,et al. Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. , 1994, Journal of molecular biology.
[99] R. Abagyan,et al. Recognition of distantly related proteins through energy calculations , 1994, Proteins.
[100] C. Frömmel,et al. Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models. , 1994, Protein engineering.
[101] J. Skolnick,et al. Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.
[102] C. Sander,et al. Correlated mutations and residue contacts in proteins , 1994, Proteins.
[103] J. Skolnick,et al. Monte carlo simulations of protein folding. I. Lattice model and interaction scheme , 1994, Proteins.
[104] C. Sander,et al. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? , 1994, Protein engineering.
[105] K. Hatrick,et al. Compensating changes in protein multiple sequence alignments. , 1994, Protein engineering.
[106] P Argos,et al. Folding the main chain of small proteins with the genetic algorithm. , 1994, Journal of molecular biology.
[107] S. Wodak,et al. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. , 1994, Journal of molecular biology.
[108] D. Covell,et al. Lattice model simulations of polypeptide chain folding. , 1994, Journal of molecular biology.
[109] L. Wyns,et al. Crystal structure of RNase T1 with 3'-guanylic acid and guanosine. , 1993, The Journal of biological chemistry.
[110] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[111] C Sander,et al. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. , 1993, Journal of molecular biology.
[112] B. Rost,et al. Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.
[113] S. Bryant,et al. An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.
[114] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[115] Shoshana J. Wodak,et al. Generating and testing protein folds , 1993 .
[116] D. Haussler,et al. Protein modeling using hidden Markov models: analysis of globins , 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.
[117] A. Godzik,et al. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[118] 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.
[119] G. Crippen,et al. Contact potential that recognizes the correct folding of globular proteins. , 1992, Journal of molecular biology.
[120] Udi Manber,et al. Fast text searching: allowing errors , 1992, CACM.
[121] A. Godzik,et al. Topology fingerprint approach to the inverse protein folding problem. , 1992, Journal of molecular biology.
[122] M. Levitt. Accurate modeling of protein conformation by automatic segment matching. , 1992, Journal of molecular biology.
[123] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[124] M. Sippl,et al. Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations , 1992, Proteins.
[125] William R. Taylor,et al. The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..
[126] C. Sander,et al. Evaluation of protein models by atomic solvation preference. , 1992, Journal of molecular biology.
[127] Rainer Fuchs,et al. CLUSTAL V: improved software for multiple sequence alignment , 1992, Comput. Appl. Biosci..
[128] M. Levitt,et al. A lattice model for protein structure prediction at low resolution. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[129] John P. Overington,et al. Environment‐specific amino acid substitution tables: Tertiary templates and prediction of protein folds , 1992, Protein science : a publication of the Protein Society.
[130] B. Finzel,et al. Crystallographic refinement of bovine pro-phospholipase A2 at 1.6 A resolution. , 1991, Acta crystallographica. Section B, Structural science.
[131] W. Miller,et al. A time-efficient, linear-space local similarity algorithm , 1991 .
[132] G. Casari,et al. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. , 1990, Journal of molecular biology.
[133] Wen-Hsiung Li,et al. Fundamentals of molecular evolution , 1990 .
[134] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[135] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[136] W R Taylor,et al. Hierarchical method to align large numbers of biological sequences. , 1990, Methods in enzymology.
[137] W. Pearson. Rapid and sensitive sequence comparison with FASTP and FASTA. , 1990, Methods in enzymology.
[138] W R Taylor,et al. Protein structure alignment. , 1989, Journal of molecular biology.
[139] S. Altschul,et al. A tool for multiple sequence alignment. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[140] A Coda,et al. Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution. , 1989, Journal of molecular biology.
[141] D. Higgins,et al. See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .
[142] F. Corpet. Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.
[143] D. Lipman,et al. The multiple sequence alignment problem in biology , 1988 .
[144] J. L. Smith,et al. Refinement at 1.4 A resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder. , 1988, Acta crystallographica. Section A, Foundations of crystallography.
[145] A. Wlodawer,et al. Structure of phosphate-free ribonuclease A refined at 1.26 A. , 1988, Biochemistry.
[146] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[147] E N Baker,et al. Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules. , 1987, Journal of molecular biology.
[148] M. Sternberg,et al. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. , 1987, Journal of molecular biology.
[149] M. Waterman,et al. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. , 1987, Journal of molecular biology.
[150] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[151] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[152] C. Bugg,et al. Structure of ubiquitin refined at 1.8 A resolution. , 1987, Journal of molecular biology.
[153] R. Huber,et al. Crystal structure determination, refinement and the molecular model of the alpha-amylase inhibitor Hoe-467A. , 1986, Journal of molecular biology.
[154] J. Moult,et al. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.
[155] J. Felsenstein. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.
[156] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[157] R J Read,et al. Critical evaluation of comparative model building of Streptomyces griseus trypsin. , 1984, Biochemistry.
[158] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[159] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[160] D. Lipman,et al. Rapid similarity searches of nucleic acid and protein data banks. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[161] M. James,et al. Structure and refinement of penicillopepsin at 1.8 A resolution. , 1983, Journal of molecular biology.
[162] R. Dickerson,et al. Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms. , 1982, Journal of molecular biology.
[163] P J Artymiuk,et al. Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions. , 1981, Journal of molecular biology.
[164] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[165] F. Lederer,et al. Improvement of the 2.5 A resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics. , 1979, Journal of molecular biology.
[166] J Deisenhofer,et al. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. , 1974, Journal of molecular biology.
[167] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[168] 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.