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For: Chiusano ML, Alvarez-Valin F, Di Giulio M, D'Onofrio G, Ammirato G, Colonna G, Bernardi G. Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 2000;261:63-9. [PMID: 11164038 DOI: 10.1016/s0378-1119(00)00521-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Number Cited by Other Article(s)
1
Majeed A, Sharma V, Ul Rehman W, Kaur A, Das S, Joseph J, Singh A, Bhardwaj P. Comprehensive Codon Usage Analysis Across Diverse Plant Lineages. Biochem Genet 2025:10.1007/s10528-025-11053-y. [PMID: 39966258 DOI: 10.1007/s10528-025-11053-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/06/2025] [Indexed: 02/20/2025]
2
O'Connor PBF. The Evolutionary Transition of the RNA World to Obcells to Cellular-Based Life. J Mol Evol 2024;92:278-285. [PMID: 38683368 DOI: 10.1007/s00239-024-10171-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/08/2024] [Indexed: 05/01/2024]
3
Di Giulio M. Theories of the origin of the genetic code: Strong corroboration for the coevolution theory. Biosystems 2024;239:105217. [PMID: 38663520 DOI: 10.1016/j.biosystems.2024.105217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
4
Štambuk N, Konjevoda P, Štambuk A. How ambiguity codes specify molecular descriptors and information flow in Code Biology. Biosystems 2023;233:105034. [PMID: 37739308 DOI: 10.1016/j.biosystems.2023.105034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
5
Štambuk N, Konjevoda P, Brčić-Kostić K, Baković J, Štambuk A. New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group. Biosystems 2023;233:105030. [PMID: 37717902 DOI: 10.1016/j.biosystems.2023.105030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
6
Caldararo F, Di Giulio M. The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships. Biosystems 2022;214:104613. [DOI: 10.1016/j.biosystems.2022.104613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 01/23/2023]
7
Schwersensky M, Rooman M, Pucci F. Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness. BMC Biol 2020;18:146. [PMID: 33081759 PMCID: PMC7576759 DOI: 10.1186/s12915-020-00870-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022]  Open
8
Codon usage bias in the H gene of canine distemper virus. Microb Pathog 2020;149:104511. [PMID: 32961282 DOI: 10.1016/j.micpath.2020.104511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022]
9
Wang B. The Pattern of Occurrence of Cytosine in the Genetic Code Minimizes Deleterious Mutations and Favors Proper Function of the Translational Machinery. OPEN JOURNAL OF GENETICS 2020;10:8-15. [DOI: 10.4236/ojgen.2020.101002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
10
Wang B. The Eight Trigrams of the I Ching Provide a New Avenue for Characterizing the Association between mRNA Codons and the Hydrophobicity of the Encoded Amino Acids. OPEN JOURNAL OF PHILOSOPHY 2020;10:1-8. [DOI: 10.4236/ojpp.2020.101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
11
Ismail SNFB, Baharum SN, Fazry S, Low CF. Comparative genome analysis reveals a distinct influence of nucleotide composition on virus-host species-specific interaction of prawn-infecting nodavirus. JOURNAL OF FISH DISEASES 2019;42:1761-1772. [PMID: 31637743 DOI: 10.1111/jfd.13093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
12
Zu H, Zhang H, Yao M, Zhang J, Di H, Zhang L, Dong L, Wang Z, Zhou Y. Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus. PLoS One 2019;14:e0224569. [PMID: 31697693 PMCID: PMC6837423 DOI: 10.1371/journal.pone.0224569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/16/2019] [Indexed: 02/04/2023]  Open
13
Fontrodona N, Aubé F, Claude JB, Polvèche H, Lemaire S, Tranchevent LC, Modolo L, Mortreux F, Bourgeois CF, Auboeuf D. Interplay between coding and exonic splicing regulatory sequences. Genome Res 2019;29:711-722. [PMID: 30962178 PMCID: PMC6499313 DOI: 10.1101/gr.241315.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 03/28/2019] [Indexed: 01/24/2023]
14
Compositional dynamics and codon usage pattern of BRCA1 gene across nine mammalian species. Genomics 2019;111:167-176. [DOI: 10.1016/j.ygeno.2018.01.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/22/2017] [Accepted: 01/22/2018] [Indexed: 11/19/2022]
15
Chakraborty S, Uddin A, Mazumder TH, Choudhury MN, Malakar AK, Paul P, Halder B, Deka H, Mazumder GA, Barbhuiya RA, Barbhuiya MA, Devi WJ. Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents. Mitochondrion 2018;42:64-76. [DOI: 10.1016/j.mito.2017.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/09/2017] [Accepted: 11/27/2017] [Indexed: 02/03/2023]
16
Li G, Ji S, Zhai X, Zhang Y, Liu J, Zhu M, Zhou J, Su S. Evolutionary and genetic analysis of the VP2 gene of canine parvovirus. BMC Genomics 2017;18:534. [PMID: 28716118 PMCID: PMC5512735 DOI: 10.1186/s12864-017-3935-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/09/2017] [Indexed: 01/20/2023]  Open
17
Chakraborty S, Nag D, Mazumder TH, Uddin A. Codon usage pattern and prediction of gene expression level in Bungarus species. Gene 2016;604:48-60. [PMID: 27845207 DOI: 10.1016/j.gene.2016.11.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 10/18/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
18
Uddin A, Choudhury MN, Chakraborty S. Codon usage bias and phylogenetic analysis of mitochondrial ND1 gene in pisces, aves, and mammals. Mitochondrial DNA A DNA Mapp Seq Anal 2016;29:36-48. [PMID: 27776434 DOI: 10.1080/24701394.2016.1233534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
19
Nasrullah I, Butt AM, Tahir S, Idrees M, Tong Y. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution. BMC Evol Biol 2015;15:174. [PMID: 26306510 PMCID: PMC4550055 DOI: 10.1186/s12862-015-0456-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023]  Open
20
Ponce de Leon M, de Miranda AB, Alvarez-Valin F, Carels N. The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins. Bioinform Biol Insights 2014;8:93-108. [PMID: 24899802 PMCID: PMC4039185 DOI: 10.4137/bbi.s13161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/24/2013] [Accepted: 11/24/2013] [Indexed: 01/02/2023]  Open
21
Butt AM, Nasrullah I, Tong Y. Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS One 2014;9:e90905. [PMID: 24595095 PMCID: PMC3942501 DOI: 10.1371/journal.pone.0090905] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/06/2014] [Indexed: 02/03/2023]  Open
22
Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1. PLoS One 2013;8:e81469. [PMID: 24303050 PMCID: PMC3841265 DOI: 10.1371/journal.pone.0081469] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/12/2013] [Indexed: 11/19/2022]  Open
23
The complete mitochondrial genome of the Antarctic sea spider Ammothea carolinensis (Chelicerata; Pycnogonida). Polar Biol 2013. [DOI: 10.1007/s00300-013-1288-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
24
Biro JC. Coding nucleic acids are chaperons for protein folding: a novel theory of protein folding. Gene 2012;515:249-57. [PMID: 23266645 DOI: 10.1016/j.gene.2012.12.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 11/29/2022]
25
Wang Q, Lei Y, Xu X, Wang G, Chen LL. Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58. PLoS One 2012;7:e43176. [PMID: 22984411 PMCID: PMC3439454 DOI: 10.1371/journal.pone.0043176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 07/18/2012] [Indexed: 11/19/2022]  Open
26
Lei Y, Kang SK, Gao J, Jia XS, Chen LL. Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A. J Biomol Struct Dyn 2012;31:342-50. [PMID: 22849520 DOI: 10.1080/07391102.2012.698218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
27
Huang JT, Xing DJ, Huang W. Choice of synonymous codons associated with protein folding. Proteins 2012;80:2056-62. [DOI: 10.1002/prot.24096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/29/2012] [Accepted: 04/05/2012] [Indexed: 11/11/2022]
28
Dass JFP, Sudandiradoss C. Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species. Gene 2012;503:92-100. [PMID: 22480817 DOI: 10.1016/j.gene.2012.03.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 03/14/2012] [Accepted: 03/17/2012] [Indexed: 11/16/2022]
29
Liu XS, Zhang YG, Fang YZ, Wang YL. Patterns and influencing factor of synonymous codon usage in porcine circovirus. Virol J 2012;9:68. [PMID: 22416942 PMCID: PMC3341187 DOI: 10.1186/1743-422x-9-68] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 03/15/2012] [Indexed: 11/11/2022]  Open
30
Yu JF, Xiao K, Jiang DK, Guo J, Wang JH, Sun X. An integrative method for identifying the over-annotated protein-coding genes in microbial genomes. DNA Res 2011;18:435-49. [PMID: 21903723 PMCID: PMC3223076 DOI: 10.1093/dnares/dsr030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
31
Zhang Z, Yu J. On the organizational dynamics of the genetic code. GENOMICS PROTEOMICS & BIOINFORMATICS 2011;9:21-9. [PMID: 21641559 PMCID: PMC5054158 DOI: 10.1016/s1672-0229(11)60004-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 10/26/2010] [Indexed: 11/23/2022]
32
Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD, Lavrov DV. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. MITOCHONDRIAL DNA 2011;22:130-42. [PMID: 21985407 PMCID: PMC3313829 DOI: 10.3109/19401736.2011.624611] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
33
Tang SL, Chang BC, Halgamuge SK. Gene functionality's influence on the second codon: A large-scale survey of second codon composition in three domains. Genomics 2010;96:92-101. [DOI: 10.1016/j.ygeno.2010.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 02/03/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
34
Agutter PS. Editorial: hypotheses about protein folding--the proteomic code and wonderfolds. THEORETICAL BIOLOGY & MEDICAL MODELLING 2009;6:31. [PMID: 20034380 PMCID: PMC2803780 DOI: 10.1186/1742-4682-6-31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 12/24/2009] [Indexed: 11/22/2022]
35
Jiang P, Sun X, Lu Z. Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms. J Genet Genomics 2009;34:275-84. [PMID: 17498625 PMCID: PMC7129909 DOI: 10.1016/s1673-8527(07)60029-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 08/22/2006] [Indexed: 11/18/2022]
36
Biro JC. Discovery of proteomic code with mRNA assisted protein folding. Int J Mol Sci 2008;9:2424-2446. [PMID: 19330085 PMCID: PMC2635648 DOI: 10.3390/ijms9122424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 11/24/2008] [Accepted: 12/02/2008] [Indexed: 01/18/2023]  Open
37
Komar AA. A pause for thought along the co-translational folding pathway. Trends Biochem Sci 2008;34:16-24. [PMID: 18996013 DOI: 10.1016/j.tibs.2008.10.002] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 10/09/2008] [Accepted: 10/13/2008] [Indexed: 11/26/2022]
38
Guo FB. The distribution patterns of bases of protein-coding genes, non-coding ORFs, and intergenic sequences in pseudomonas aeruginosa PA01 genome and its implications. J Biomol Struct Dyn 2008;25:127-33. [PMID: 17718591 DOI: 10.1080/07391102.2007.10507161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
39
Chen LL, Ma BG, Gao N. Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043. FEBS J 2007;275:198-206. [PMID: 18067578 DOI: 10.1111/j.1742-4658.2007.06190.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
40
Moura GR, Lousado JP, Pinheiro M, Carreto L, Silva RM, Oliveira JL, Santos MAS. Codon-triplet context unveils unique features of the Candida albicans protein coding genome. BMC Genomics 2007;8:444. [PMID: 18047667 PMCID: PMC2244636 DOI: 10.1186/1471-2164-8-444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 11/29/2007] [Indexed: 11/29/2022]  Open
41
Biro JC. The Proteomic Code: a molecular recognition code for proteins. Theor Biol Med Model 2007;4:45. [PMID: 17999762 PMCID: PMC2206014 DOI: 10.1186/1742-4682-4-45] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2007] [Accepted: 11/13/2007] [Indexed: 11/30/2022]  Open
42
Comparative analysis of essential genes and nonessential genes in Escherichia coli K12. Mol Genet Genomics 2007;279:87-94. [PMID: 17943314 DOI: 10.1007/s00438-007-0298-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
43
Biro JC. Protein folding information in nucleic acids which is not present in the genetic code. Ann N Y Acad Sci 2007;1091:399-411. [PMID: 17341631 DOI: 10.1196/annals.1378.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
44
Yang J, Dong XC, Leng Y. Application of FTTP to alpha-helix or beta-strand motifs. J Theor Biol 2006;242:199-219. [PMID: 16616204 DOI: 10.1016/j.jtbi.2006.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2005] [Revised: 02/17/2006] [Accepted: 02/21/2006] [Indexed: 11/28/2022]
45
Biro JC. Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases. Theor Biol Med Model 2006;3:28. [PMID: 16893453 PMCID: PMC1560374 DOI: 10.1186/1742-4682-3-28] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 08/07/2006] [Indexed: 12/02/2022]  Open
46
Yang J, Dong XC, Leng Y. Conformation biases of amino acids based on tripeptide microenvironment from PDB database. J Theor Biol 2005;240:374-84. [PMID: 16290902 DOI: 10.1016/j.jtbi.2005.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/30/2022]
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Sau K, Gupta SK, Sau S, Ghosh TC. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Res 2005;113:123-31. [PMID: 15970346 DOI: 10.1016/j.virusres.2005.05.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 05/06/2005] [Accepted: 05/10/2005] [Indexed: 11/22/2022]
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Bradshaw PC, Rathi A, Samuels DC. Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich. BMC Genomics 2005;6:136. [PMID: 16185363 PMCID: PMC1262711 DOI: 10.1186/1471-2164-6-136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 09/26/2005] [Indexed: 11/10/2022]  Open
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Biro JC. Nucleic acid chaperons: a theory of an RNA-assisted protein folding. Theor Biol Med Model 2005;2:35. [PMID: 16137324 PMCID: PMC1232867 DOI: 10.1186/1742-4682-2-35] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2005] [Accepted: 09/01/2005] [Indexed: 12/04/2022]  Open
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Sau K, Sau S, Mandal SC, Ghosh TC. Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ. Acta Biochim Biophys Sin (Shanghai) 2005;37:625-33. [PMID: 16143818 PMCID: PMC7109957 DOI: 10.1111/j.1745-7270.2005.00089.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
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