These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
232 related articles for article (PubMed ID: 25473967)
1. The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets. Ferrada E PLoS Comput Biol; 2014 Dec; 10(12):e1003946. PubMed ID: 25473967 [TBL] [Abstract][Full Text] [Related]
2. Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment. Peterson EL; Kondev J; Theriot JA; Phillips R Bioinformatics; 2009 Jun; 25(11):1356-62. PubMed ID: 19351620 [TBL] [Abstract][Full Text] [Related]
3. Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds. Solis AD BMC Evol Biol; 2019 Jul; 19(1):158. PubMed ID: 31362700 [TBL] [Abstract][Full Text] [Related]
4. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Babajide A; Hofacker IL; Sippl MJ; Stadler PF Fold Des; 1997; 2(5):261-9. PubMed ID: 9261065 [TBL] [Abstract][Full Text] [Related]
5. Protein design under competing conditions for the availability of amino acids. Nerattini F; Tubiana L; Cardelli C; Bianco V; Dellago C; Coluzza I Sci Rep; 2020 Feb; 10(1):2684. PubMed ID: 32060385 [TBL] [Abstract][Full Text] [Related]
6. Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids. Tanaka J; Doi N; Takashima H; Yanagawa H Protein Sci; 2010 Apr; 19(4):786-95. PubMed ID: 20162614 [TBL] [Abstract][Full Text] [Related]
7. Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Melo F; Marti-Renom MA Proteins; 2006 Jun; 63(4):986-95. PubMed ID: 16506243 [TBL] [Abstract][Full Text] [Related]
8. Protein language models meet reduced amino acid alphabets. Ieremie I; Ewing RM; Niranjan M Bioinformatics; 2024 Feb; 40(2):. PubMed ID: 38310333 [TBL] [Abstract][Full Text] [Related]
9. Sequence-dependent and -independent information in a combined random energy model for protein folding and coding. Pereira de Araújo AF Proteins; 2024 May; 92(5):679-687. PubMed ID: 38158239 [TBL] [Abstract][Full Text] [Related]
10. Automated alphabet reduction for protein datasets. Bacardit J; Stout M; Hirst JD; Valencia A; Smith RE; Krasnogor N BMC Bioinformatics; 2009 Jan; 10():6. PubMed ID: 19126227 [TBL] [Abstract][Full Text] [Related]
11. Simplified amino acid alphabets for protein fold recognition and implications for folding. Murphy LR; Wallqvist A; Levy RM Protein Eng; 2000 Mar; 13(3):149-52. PubMed ID: 10775656 [TBL] [Abstract][Full Text] [Related]
12. Non-intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns. Hennetin J; Le TK; Canard L; Colloc'h N; Mornon JP; Callebaut I Proteins; 2003 May; 51(2):236-44. PubMed ID: 12660992 [TBL] [Abstract][Full Text] [Related]
13. Comparing folding codes for proteins and polymers. Chan HS; Dill KA Proteins; 1996 Mar; 24(3):335-44. PubMed ID: 8778780 [TBL] [Abstract][Full Text] [Related]
14. Protein design with L- and D-alpha-amino acid structures as the alphabet. Durani S Acc Chem Res; 2008 Oct; 41(10):1301-8. PubMed ID: 18642934 [TBL] [Abstract][Full Text] [Related]
15. Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins. Solis AD Proteins; 2015 Dec; 83(12):2198-216. PubMed ID: 26407535 [TBL] [Abstract][Full Text] [Related]
17. Reduced alphabet for protein folding prediction. Huang JT; Wang T; Huang SR; Li X Proteins; 2015 Apr; 83(4):631-9. PubMed ID: 25641420 [TBL] [Abstract][Full Text] [Related]
18. Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet. Suárez-Diez M; Pujol AM; Matzapetakis M; Jaramillo A; Iranzo O Biotechnol J; 2013 Jul; 8(7):855-64. PubMed ID: 23788466 [TBL] [Abstract][Full Text] [Related]
19. Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures. Mirzaie M Amino Acids; 2019 Jul; 51(7):1029-1038. PubMed ID: 31098784 [TBL] [Abstract][Full Text] [Related]
20. Size and structure of the sequence space of repeat proteins. Marchi J; Galpern EA; Espada R; Ferreiro DU; Walczak AM; Mora T PLoS Comput Biol; 2019 Aug; 15(8):e1007282. PubMed ID: 31415557 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]