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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1963 1
1967 1
1969 1
1970 4
1971 1
1972 2
1974 5
1975 13
1976 18
1977 22
1978 4
1979 19
1980 19
1981 11
1982 18
1983 27
1984 35
1985 41
1986 50
1987 58
1988 62
1989 89
1990 111
1991 171
1992 203
1993 221
1994 287
1995 287
1996 297
1997 301
1998 312
1999 322
2000 364
2001 336
2002 346
2003 334
2004 363
2005 377
2006 356
2007 392
2008 350
2009 326
2010 286
2011 322
2012 299
2013 265
2014 265
2015 262
2016 244
2017 228
2018 198
2019 202
2020 212
2021 190
2022 171
2023 144
2024 62

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9,263 results

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Page 1
Amino acid contact energy networks impact protein structure and evolution.
Yan W, Sun M, Hu G, Zhou J, Zhang W, Chen J, Chen B, Shen B. Yan W, et al. J Theor Biol. 2014 Aug 21;355:95-104. doi: 10.1016/j.jtbi.2014.03.032. Epub 2014 Apr 1. J Theor Biol. 2014. PMID: 24703984
One of the most challenging tasks in structural proteomics is to understand the relationship between protein structure, biological function, and evolution. An understanding of amino acid networks based on protein topology has an important role in the study of this r …
One of the most challenging tasks in structural proteomics is to understand the relationship between protein structure, biological function, …
An amino acid map of inter-residue contact energies using metric multi-dimensional scaling.
Rakshit S, Ananthasuresh GK. Rakshit S, et al. J Theor Biol. 2008 Jan 21;250(2):291-7. doi: 10.1016/j.jtbi.2007.09.032. Epub 2007 Sep 26. J Theor Biol. 2008. PMID: 17981305
This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact energies imply the hydrophobic-hydrophilic nature of the amino acid residues. ...We also use a hierarchical cluster …
This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact …
Enhancing protein contact map prediction accuracy via ensembles of inter-residue distance predictors.
Newton MAH, Rahman J, Zaman R, Sattar A. Newton MAH, et al. Comput Biol Chem. 2022 Aug;99:107700. doi: 10.1016/j.compbiolchem.2022.107700. Epub 2022 May 23. Comput Biol Chem. 2022. PMID: 35665657
Protein contact maps capture coevolutionary interactions between amino acid residue pairs that are spatially within certain proximity threshold. ...Contact map prediction has achieved significant progress lately but still further challenges rema …
Protein contact maps capture coevolutionary interactions between amino acid residue pairs that are spatially wit …
Identification of residue pairing in interacting beta-strands from a predicted residue contact map.
Mao W, Wang T, Zhang W, Gong H. Mao W, et al. BMC Bioinformatics. 2018 Apr 19;19(1):146. doi: 10.1186/s12859-018-2150-1. BMC Bioinformatics. 2018. PMID: 29673311 Free PMC article.
BACKGROUND: Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. ...In this work, we propose a novel ridge-detection-based beta-beta contact predictor to identify res …
BACKGROUND: Despite the rapid progress of protein residue contact prediction, predicted residue contact maps fre …
Amino acid distribution rules predict protein fold.
Kister AE, Potapov V. Kister AE, et al. Biochem Soc Trans. 2013 Apr;41(2):616-9. doi: 10.1042/BST20120308. Biochem Soc Trans. 2013. PMID: 23514164 Review.
The residue distribution rules specify the 'favourable' residues that are required in certain positions of a polypeptide chain in order for it to assume a particular protein fold, and the 'unfavourable' residues incompatible with the given fold. Identificatio …
The residue distribution rules specify the 'favourable' residues that are required in certain positions of a polypeptide chain …
Amino acid residue environments and predictions of residue type.
Kim W, Wilbur WJ. Kim W, et al. Comput Chem. 2001 Jul;25(4):411-22. doi: 10.1016/s0097-8485(01)00075-4. Comput Chem. 2001. PMID: 11459355
One approach to this problem that has shown promise and given a measure of success is threading. In this approach contact energies between different amino acids are first determined by statistical methods applied to known structures. ...Here, we investigate t …
One approach to this problem that has shown promise and given a measure of success is threading. In this approach contact energies be …
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates.
Villegas JA, Levy ED. Villegas JA, et al. Protein Sci. 2022 Jul;31(7):e4361. doi: 10.1002/pro.4361. Protein Sci. 2022. PMID: 35762716 Free PMC article.
This result implies that selective trafficking of client proteins to distinct membraneless organelles requires recognition elements beyond the client sequence composition. STATEMENT: Empirical potentials for amino acid stickiness and pairwise residue conta …
This result implies that selective trafficking of client proteins to distinct membraneless organelles requires recognition elements beyond t …
Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins.
Mallik S, Kundu S. Mallik S, et al. Genome Biol Evol. 2017 Apr 1;9(4):916-931. doi: 10.1093/gbe/evx036. Genome Biol Evol. 2017. PMID: 28338825 Free PMC article.
The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino a …
The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nuc …
Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.
Fokas AS, Cole DJ, Ahnert SE, Chin AW. Fokas AS, et al. Sci Rep. 2016 Sep 14;6:33213. doi: 10.1038/srep33213. Sci Rep. 2016. PMID: 27623708 Free PMC article.
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. ...Furthermore, among residues with high closeness, those with low degree were particularly stro …
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can pr …
CONFOLD: Residue-residue contact-guided ab initio protein folding.
Adhikari B, Bhattacharya D, Cao R, Cheng J. Adhikari B, et al. Proteins. 2015 Aug;83(8):1436-49. doi: 10.1002/prot.24829. Epub 2015 Jun 6. Proteins. 2015. PMID: 25974172 Free PMC article.
Predicted protein residue-residue contacts can be used to build three-dimensional models and consequently to predict protein folds from scratch. A considerable amount of effort is currently being spent to improve contact prediction accuracy, whereas fe …
Predicted protein residue-residue contacts can be used to build three-dimensional models and consequently to predict pr …
9,263 results