Fold and function predictions for Mycoplasma genitalium proteins
Tài liệu tham khảo
Altschul, 1990, Basic local alignment search tool, J. Mol. Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
Pearson, 1992, Dynamic programming algorithms for biological sequence comparison, Methods Enzymol, 210, 575, 10.1016/0076-6879(92)10029-D
Wisconsin Package Version 9, Genetics Computer Group (GCG), Madison, Wisconsin, USA. World Wide Web URL: www.gcg.com.
Geourjon, 1995, ANTHEPROT 2.0: a three-dimensional module fully coupled with protein sequence analysis methods, J. Mol. Graphics, 13, 209, 10.1016/0263-7855(95)00035-5
(1996). SWISSMODEL, an automated knowledge based modelling server. World Wide Web URL: http://expasy.hcuge.ch/swissmod/swiss-model.html.
Henikoff, 1998, Superior performance in protein homology detection with the BLOCKS database server, Nucleic Acids Res, 26, 309, 10.1093/nar/26.1.309
Bowie, 1991, A method to identify protein sequences that fold into a known three dimensional structure, Science, 253, 164, 10.1126/science.1853201
Jones, 1992, A new approach to protein fold recognition, Nature, 358, 86, 10.1038/358086a0
Godzik, 1992, A topology fingerprint approach to the inverse folding problem, J. Mol. Biol, 227, 227, 10.1016/0022-2836(92)90693-E
Sippl, 1992, Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations, Proteins, 13, 258, 10.1002/prot.340130308
Bryant, 1993, An empirical energy function for threading protein sequence through folding motif, Proteins, 16, 92, 10.1002/prot.340160110
Gribskov, 1987, Profile analysis: detection of distantly related proteins, Proc. Natl Acad. Sci. USA, 84, 4355, 10.1073/pnas.84.13.4355
Bork, 1996, Applying motif and profile searches, Methods Enzymol, 266, 162, 10.1016/S0076-6879(96)66013-3
Rychlewski, 1998, Comparison of sequence profiles. Structural predictions with no structure information, Protein Sci
Pastore, 1990, Comparison of the structure of globins and phycocyanins: evidence for evolutionary relationship, Proteins, 8, 133, 10.1002/prot.340080204
Holm, 1995, Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme, EMBO J, 14, 1287, 10.1002/j.1460-2075.1995.tb07114.x
Babbitt, 1995, Functionally diverse enzyme superfamily that abstracts the α proton of carboxylic acids, Science, 267, 1159, 10.1126/science.7855594
Murzin, 1997, Distant homology recognition using structural classification of proteins, Proteins, 105, 10.1002/(SICI)1097-0134(1997)1+<105::AID-PROT14>3.0.CO;2-S
Karplus, 1997, Predicting protein structure using Hidden Markov Models, Proteins, 134, 10.1002/(SICI)1097-0134(1997)1+<134::AID-PROT18>3.0.CO;2-P
Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acid Res, 25, 3389, 10.1093/nar/25.17.3389
Fischer, 1997, Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium, Proc. Natl Acad. Sci. USA, 94, 11929, 10.1073/pnas.94.22.11929
Jaroszewski, 1998, Fold prediction by a hierarchy of sequence and threading methods, Protein Sci, 10.1002/pro.5560070620
Fraser, 1995, The minimal gene complement of Mycoplasma genitalium, Science, 270, 397, 10.1126/science.270.5235.397
Moult, 1996, The current state of the art in protein structure prediction, Curr. Opin. Biotechnol, 7, 422, 10.1016/S0958-1669(96)80118-2
Francklyn, 1997, Aminoacyl-tRNA synthetases in biology and disease: new evidence for structural and functional diversity in an ancient family of enzymes, RNA, 3, 954
Lodmell, 1997, A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA, Science, 277, 1262, 10.1126/science.277.5330.1262
Sette, 1997, The structure of the translational initiation factor IF1 from E. coli contains an oligomer binding motif, EMBO J, 16, 1436, 10.1093/emboj/16.6.1436
Hubbard, 1997, SCOP: a structural classification of the protein database, Nucleic Acids Res, 25, 236, 10.1093/nar/25.1.236
Ouzounis, 1993, Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures, J. Mol. Biol, 232, 805, 10.1006/jmbi.1993.1433
Pearson, 1997, Identifying distantly related protein sequences, Comput. Appl. Biosci, 13, 325
Ceska, 1996, A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease, Nature, 382, 90, 10.1038/382090a0
Šali, 1995, Evaluation of comparative protein modeling by MODELLER, Proteins, 23, 318, 10.1002/prot.340230306
Martin, 1980, Differentiation of mycoplasmalates from bacterial protoplast L-forms by assay for penicillin binding, Arch. Microbiol, 127, 297, 10.1007/BF00427207
Waterman, 1995
Gonnet, 1992, Analysis of amino acid substitution during divergent evolution, Science, 256, 1443, 10.1126/science.1604319
Karlin, 1990, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes, Proc. Natl Acad. Sci. USA, 87, 2264, 10.1073/pnas.87.6.2264