TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1993 DA - 1993// TI - Performance evaluation of amino acid substitution matrices JO - Proteins VL - 17 UR - https://doi.org/10.1002/prot.340170108 DO - 10.1002/prot.340170108 ID - Henikoff1993 ER - TY - JOUR AU - Jeanmougin, F. AU - Thompson, J. D. AU - Gouy, M. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1998 DA - 1998// TI - Multiple sequence alignment with Clustal X JO - Trends Biochem Sci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01285-7 DO - 10.1016/S0968-0004(98)01285-7 ID - Jeanmougin1998 ER - TY - CHAP AU - Tress, M. AU - Ezkurdia, I. AU - Grana, O. AU - Lopez, G. AU - Valencia, A. PY - 2005 DA - 2005// TI - Assessment of predictions submitted for the CASP6 comparative modelling category BT - Proteins ID - Tress2005 ER - TY - JOUR AU - Vilim, R. B. AU - Cunningham, R. M. AU - Lu, B. AU - Kheradpour, P. AU - Stevens, F. J. PY - 2004 DA - 2004// TI - Fold-specific substitution matrices for protein classification JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg492 DO - 10.1093/bioinformatics/btg492 ID - Vilim2004 ER - TY - JOUR AU - Teodorescu, O. AU - Galor, T. AU - Pillardy, J. AU - Elber, R. PY - 2004 DA - 2004// TI - Enriching the sequence substitution matrix by structural information JO - Proteins VL - 54 UR - https://doi.org/10.1002/prot.10474 DO - 10.1002/prot.10474 ID - Teodorescu2004 ER - TY - JOUR AU - Bastien, O. AU - Roy, S. AU - Marechal, E. PY - 2005 DA - 2005// TI - Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions JO - C R Biol VL - 328 UR - https://doi.org/10.1016/j.crvi.2005.02.002 DO - 10.1016/j.crvi.2005.02.002 ID - Bastien2005 ER - TY - JOUR AU - Jones, D. T. AU - Taylor, W. R. AU - Thornton, J. M. PY - 1994 DA - 1994// TI - A mutation data matrix for transmembrane proteins JO - FEBS Letters VL - 339 UR - https://doi.org/10.1016/0014-5793(94)80429-X DO - 10.1016/0014-5793(94)80429-X ID - Jones1994 ER - TY - JOUR AU - Sutormin, R. A. AU - Rakhmaninova, A. B. AU - Gelfand, M. S. PY - 2003 DA - 2003// TI - BATMAS30: amino acid substitution matrix for alignment of bacterial transporters JO - Proteins VL - 51 UR - https://doi.org/10.1002/prot.10308 DO - 10.1002/prot.10308 ID - Sutormin2003 ER - TY - JOUR AU - Pacholczyk, M. AU - Kimmel, M. PY - 2005 DA - 2005// TI - Analysis of differences in amino acid substitution patterns, using multilevel G-tests JO - C R Biol VL - 328 UR - https://doi.org/10.1016/j.crvi.2005.03.003 DO - 10.1016/j.crvi.2005.03.003 ID - Pacholczyk2005 ER - TY - JOUR AU - Yu, Y. K. AU - Altschul, S. F. PY - 2005 DA - 2005// TI - The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti070 DO - 10.1093/bioinformatics/bti070 ID - Yu2005 ER - TY - JOUR AU - Adachi, J. AU - Hasegawa, M. PY - 1996 DA - 1996// TI - Model of amino acid substitution in proteins encoded by mitochondrial DNA JO - J Mol Evol VL - 42 UR - https://doi.org/10.1007/BF02498640 DO - 10.1007/BF02498640 ID - Adachi1996 ER - TY - JOUR AU - Feldman, H. J. AU - Dumontier, M. AU - Ling, S. AU - Haider, N. AU - Hogue, C. W. PY - 2005 DA - 2005// TI - CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules JO - FEBS Letters VL - 579 UR - https://doi.org/10.1016/j.febslet.2005.07.039 DO - 10.1016/j.febslet.2005.07.039 ID - Feldman2005 ER - TY - JOUR AU - Giaever, G. AU - Flaherty, P. AU - Kumm, J. AU - Proctor, M. AU - Nislow, C. AU - Jaramillo, D. F. AU - Chu, A. M. AU - Jordan, M. I. AU - Arkin, A. P. AU - Davis, R. W. PY - 2004 DA - 2004// TI - Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0307490100 DO - 10.1073/pnas.0307490100 ID - Giaever2004 ER - TY - JOUR AU - di Bernardo, D. AU - Thompson, M. J. AU - Gardner, T. S. AU - Chobot, S. E. AU - Eastwood, E. L. AU - Wojtovich, A. P. AU - Elliott, S. J. AU - Schaus, S. E. AU - Collins, J. J. PY - 2005 DA - 2005// TI - Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks JO - Nature Biotechnology VL - 23 UR - https://doi.org/10.1038/nbt1075 DO - 10.1038/nbt1075 ID - di Bernardo2005 ER - TY - JOUR AU - Grantham, R. PY - 1974 DA - 1974// TI - Amino acid difference formula to help explain protein evolution JO - Science VL - 185 UR - https://doi.org/10.1126/science.185.4154.862 DO - 10.1126/science.185.4154.862 ID - Grantham1974 ER - TY - JOUR AU - Benner, S. A. AU - Cohen, M. A. AU - Gonnet, G. H. PY - 1994 DA - 1994// TI - Amino acid substitution during functionally constrained divergent evolution of protein sequences JO - Protein Eng VL - 11 UR - https://doi.org/10.1093/protein/7.11.1323 DO - 10.1093/protein/7.11.1323 ID - Benner1994 ER - TY - JOUR AU - Fitch, W. M. PY - 1966 DA - 1966// TI - An improved method of testing for evolutionary homology JO - J Mol Biol VL - 16 UR - https://doi.org/10.1016/S0022-2836(66)80258-9 DO - 10.1016/S0022-2836(66)80258-9 ID - Fitch1966 ER - TY - JOUR AU - Schneider, A. AU - Cannarozzi, G. M. AU - Gonnet, G. H. PY - 2005 DA - 2005// TI - Empirical codon substitution matrix JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-134 DO - 10.1186/1471-2105-6-134 ID - Schneider2005 ER - TY - CHAP AU - Fujitsuka, Y. AU - Chikenji, G. AU - Takada, S. PY - 2005 DA - 2005// TI - SimFold energy function for de novo protein structure prediction: Consensus with Rosetta BT - Proteins ID - Fujitsuka2005 ER - TY - JOUR AU - Yampolsky, L. Y. AU - Stoltzfus, A. PY - 2005 DA - 2005// TI - The exchangeability of amino acids in proteins JO - Genetics VL - 170 UR - https://doi.org/10.1534/genetics.104.039107 DO - 10.1534/genetics.104.039107 ID - Yampolsky2005 ER - TY - JOUR AU - Dosztanyi, Z. AU - Torda, A. E. PY - 2001 DA - 2001// TI - Amino acid similarity matrices based on force fields JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.686 DO - 10.1093/bioinformatics/17.8.686 ID - Dosztanyi2001 ER - TY - JOUR AU - Nakai, K. AU - Kidera, A. AU - Kanehisa, M. PY - 1988 DA - 1988// TI - Cluster analysis of amino acid indices for prediction of protein structure and function JO - Protein Eng VL - 2 UR - https://doi.org/10.1093/protein/2.2.93 DO - 10.1093/protein/2.2.93 ID - Nakai1988 ER - TY - JOUR AU - Tomii, K. AU - Kanehisa, M. PY - 1996 DA - 1996// TI - Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins JO - Protein Eng VL - 9 UR - https://doi.org/10.1093/protein/9.1.27 DO - 10.1093/protein/9.1.27 ID - Tomii1996 ER - TY - JOUR AU - Kawashima, S. AU - Kanehisa, M. PY - 2000 DA - 2000// TI - AAindex: amino acid index database JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.374 DO - 10.1093/nar/28.1.374 ID - Kawashima2000 ER - TY - JOUR AU - Gilis, D. AU - Massar, S. AU - Cerf, N. J. AU - Rooman, M. PY - 2001 DA - 2001// TI - Optimality of the genetic code with respect to protein stability and amino-acid frequencies JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-11-research0049 DO - 10.1186/gb-2001-2-11-research0049 ID - Gilis2001 ER - TY - BOOK AU - Tollis, I. G. AU - Tamassia, R. AU - Eades, P. AU - Di Battista, G. PY - 1998 DA - 1998// TI - Graph Drawing: Algorithms for the Visualization of Graphs ID - Tollis1998 ER - TY - STD TI - TouchGraph Website[http://www.touchgraph.com] UR - http://www.touchgraph.com ID - ref27 ER - TY - BOOK AU - Cormen, T. H. AU - Leiserson, C. E. AU - Rivest, R. L. AU - Stein, C. PY - 2001 DA - 2001// TI - Introduction to Algorithms ID - Cormen2001 ER - TY - BOOK AU - Mitchell, T. M. PY - 1997 DA - 1997// TI - Machine Learning ID - Mitchell1997 ER - TY - STD TI - AAindex Website[http://www.genome.ad.jp/dbget/aaindex.html] UR - http://www.genome.ad.jp/dbget/aaindex.html ID - ref30 ER - TY - JOUR AU - Woese, C. R. PY - 1973 DA - 1973// TI - Evolution of the genetic code JO - Naturwissenschaften VL - 60 UR - https://doi.org/10.1007/BF00592854 DO - 10.1007/BF00592854 ID - Woese1973 ER - TY - JOUR AU - Haig, D. AU - Hurst, L. D. PY - 1991 DA - 1991// TI - A quantitative measure of error minimisation within the genetic code JO - J Mol Evol VL - 33 UR - https://doi.org/10.1007/BF02103132 DO - 10.1007/BF02103132 ID - Haig1991 ER - TY - JOUR AU - Freeland, S. J. AU - Hurst, L. D. PY - 1998 DA - 1998// TI - The genetic code is one in a million JO - J Mol Evol VL - 47 UR - https://doi.org/10.1007/PL00006381 DO - 10.1007/PL00006381 ID - Freeland1998 ER - TY - JOUR AU - Goodarzi, H. AU - Shateri Najafabadi, H. AU - Torabi, N. PY - 2005 DA - 2005// TI - On the coevolution of genes and genetic code JO - Gene VL - 362 UR - https://doi.org/10.1016/j.gene.2005.08.005 DO - 10.1016/j.gene.2005.08.005 ID - Goodarzi2005 ER - TY - JOUR AU - Freeland, S. J. AU - Wu, T. AU - Keulmann, N. PY - 2003 DA - 2003// TI - The case for an Error Minimizing Standard Genetic Code JO - Orig Life Evol Biosph VL - 33 UR - https://doi.org/10.1023/A:1025771327614 DO - 10.1023/A:1025771327614 ID - Freeland2003 ER - TY - JOUR AU - Woese, C. R. AU - Dugre, D. H. AU - Saxinger, W. C. AU - Dugre, S. A. PY - 1966 DA - 1966// TI - On the fundamental nature and evolution of the genetic code JO - Cold Spring Harb Symp Quant Biol VL - 31 UR - https://doi.org/10.1101/SQB.1966.031.01.093 DO - 10.1101/SQB.1966.031.01.093 ID - Woese1966 ER - TY - JOUR AU - Kyte, J. AU - Doolittle, R. F. PY - 1982 DA - 1982// TI - A simple measure for displaying the hydropathic character of a protein JO - J Mol Biol VL - 157 UR - https://doi.org/10.1016/0022-2836(82)90515-0 DO - 10.1016/0022-2836(82)90515-0 ID - Kyte1982 ER - TY - JOUR AU - Di Giulio, M. PY - 2001 DA - 2001// TI - The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analyses tautologous JO - J Theor Biol VL - 208 UR - https://doi.org/10.1006/jtbi.2000.2206 DO - 10.1006/jtbi.2000.2206 ID - Di Giulio2001 ER - TY - JOUR AU - Szathmary, E. AU - Zintzaras, E. PY - 1992 DA - 1992// TI - A statistical test of hypotheses on the organization and origin of the genetic code JO - J Mol Evol VL - 35 UR - https://doi.org/10.1007/BF00178593 DO - 10.1007/BF00178593 ID - Szathmary1992 ER - TY - JOUR AU - Haig, D. AU - Hurst, L. D. PY - 1999 DA - 1999// TI - A quantitative measure of error minimization in the genetic code JO - J Mol Evol VL - 49 UR - https://doi.org/10.1007/PL00006591 DO - 10.1007/PL00006591 ID - Haig1999 ER - TY - JOUR AU - Ardell, D. H. PY - 1998 DA - 1998// TI - On error minimization in a sequential origin of the standard genetic code JO - J Mol Evol VL - 47 UR - https://doi.org/10.1007/PL00006356 DO - 10.1007/PL00006356 ID - Ardell1998 ER -