176 related articles for article (PubMed ID: 35060221)
1. Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences.
Holland J; Grigoryan G
Protein Sci; 2022 Apr; 31(4):900-917. PubMed ID: 35060221
[TBL] [Abstract][Full Text] [Related]
2. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.
Mukherjee A; Bagchi B
J Chem Phys; 2004 Jan; 120(3):1602-12. PubMed ID: 15268287
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Sequence statistics of tertiary structural motifs reflect protein stability.
Zheng F; Grigoryan G
PLoS One; 2017; 12(5):e0178272. PubMed ID: 28552940
[TBL] [Abstract][Full Text] [Related]
5. An empirical energy function for threading protein sequence through the folding motif.
Bryant SH; Lawrence CE
Proteins; 1993 May; 16(1):92-112. PubMed ID: 8497488
[TBL] [Abstract][Full Text] [Related]
6. Properties of contact matrices induced by pairwise interactions in proteins.
Miyazawa S; Kinjo AR
Phys Rev E Stat Nonlin Soft Matter Phys; 2008 May; 77(5 Pt 1):051910. PubMed ID: 18643105
[TBL] [Abstract][Full Text] [Related]
7. Novel knowledge-based mean force potential at atomic level.
Melo F; Feytmans E
J Mol Biol; 1997 Mar; 267(1):207-22. PubMed ID: 9096219
[TBL] [Abstract][Full Text] [Related]
8. Another look at the conditions for the extraction of protein knowledge-based potentials.
Betancourt MR
Proteins; 2009 Jul; 76(1):72-85. PubMed ID: 19089977
[TBL] [Abstract][Full Text] [Related]
9. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design.
Bordner AJ
BMC Bioinformatics; 2010 Apr; 11():192. PubMed ID: 20398384
[TBL] [Abstract][Full Text] [Related]
10. Free energies of amino acid side-chain rotamers in alpha-helices, beta-sheets and alpha-helix N-caps.
Stapley BJ; Doig AJ
J Mol Biol; 1997 Sep; 272(3):456-64. PubMed ID: 9325103
[TBL] [Abstract][Full Text] [Related]
11. Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.
Zhu H; Braun W
Protein Sci; 1999 Feb; 8(2):326-42. PubMed ID: 10048326
[TBL] [Abstract][Full Text] [Related]
12. Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization.
Sengupta D; Kundu S
BMC Bioinformatics; 2012 Jun; 13():142. PubMed ID: 22720789
[TBL] [Abstract][Full Text] [Related]
13. Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment.
Heo M; Kim S; Moon EJ; Cheon M; Chung K; Chang I
Phys Rev E Stat Nonlin Soft Matter Phys; 2005 Jul; 72(1 Pt 1):011906. PubMed ID: 16090000
[TBL] [Abstract][Full Text] [Related]
14. Identifying sequence-structure pairs undetected by sequence alignments.
Miyazawa S; Jernigan RL
Protein Eng; 2000 Jul; 13(7):459-75. PubMed ID: 10906342
[TBL] [Abstract][Full Text] [Related]
15. Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.
Zimmermann MT; Leelananda SP; Gniewek P; Feng Y; Jernigan RL; Kloczkowski A
J Struct Funct Genomics; 2011 Jul; 12(2):137-47. PubMed ID: 21674234
[TBL] [Abstract][Full Text] [Related]
16. Explicit orientation dependence in empirical potentials and its significance to side-chain modeling.
Ma J
Acc Chem Res; 2009 Aug; 42(8):1087-96. PubMed ID: 19445451
[TBL] [Abstract][Full Text] [Related]
17. Evaluation performance of substitution matrices, based on contacts between residue terminal groups.
Vishnepolsky B; Managadze G; Grigolava M; Pirtskhalava M
J Biomol Struct Dyn; 2012; 30(2):180-90. PubMed ID: 22702729
[TBL] [Abstract][Full Text] [Related]
18. Information and discrimination in pairwise contact potentials.
Solis AD; Rackovsky S
Proteins; 2008 May; 71(3):1071-87. PubMed ID: 18004788
[TBL] [Abstract][Full Text] [Related]
19. Amino acid residue environments and predictions of residue type.
Kim W; Wilbur WJ
Comput Chem; 2001 Jul; 25(4):411-22. PubMed ID: 11459355
[TBL] [Abstract][Full Text] [Related]
20. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space.
Miyazawa S; Jernigan RL
Proteins; 2003 Jan; 50(1):35-43. PubMed ID: 12471597
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
