183 related articles for article (PubMed ID: 24999015)
1. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition.
Yu H; Zhou P; Deng M; Shang Z
J Chem Inf Model; 2014 Jul; 54(7):2022-32. PubMed ID: 24999015
[TBL] [Abstract][Full Text] [Related]
2. DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.
Antes I
Proteins; 2010 Apr; 78(5):1084-104. PubMed ID: 20017216
[TBL] [Abstract][Full Text] [Related]
3. The structural basis of peptide-protein binding strategies.
London N; Movshovitz-Attias D; Schueler-Furman O
Structure; 2010 Feb; 18(2):188-99. PubMed ID: 20159464
[TBL] [Abstract][Full Text] [Related]
4. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
Liu Z; Dominy BN; Shakhnovich EI
J Am Chem Soc; 2004 Jul; 126(27):8515-28. PubMed ID: 15238009
[TBL] [Abstract][Full Text] [Related]
5. Thermodynamic consequences of stapling side-chains on a peptide ligand using a lactam-bridge: A theoretical study on anti-angiogenic peptides targeting VEGF.
Kalathingal M; Rhee YM
Proteins; 2024 Aug; 92(8):959-974. PubMed ID: 38602129
[TBL] [Abstract][Full Text] [Related]
6. Self-binding peptides: Binding-upon-folding versus folding-upon-binding.
Li Z; Yan F; Miao Q; Meng Y; Wen L; Jiang Q; Zhou P
J Theor Biol; 2019 May; 469():25-34. PubMed ID: 30802465
[TBL] [Abstract][Full Text] [Related]
7. Structural and dynamic determinants of protein-peptide recognition.
Dagliyan O; Proctor EA; D'Auria KM; Ding F; Dokholyan NV
Structure; 2011 Dec; 19(12):1837-45. PubMed ID: 22153506
[TBL] [Abstract][Full Text] [Related]
8. All-atom Monte Carlo approach to protein-peptide binding.
Staneva I; Wallin S
J Mol Biol; 2009 Nov; 393(5):1118-28. PubMed ID: 19733177
[TBL] [Abstract][Full Text] [Related]
9. Is protein context responsible for peptide-mediated interactions?
Zhou P; Miao Q; Yan F; Li Z; Jiang Q; Wen L; Meng Y
Mol Omics; 2019 Aug; 15(4):280-295. PubMed ID: 31112188
[TBL] [Abstract][Full Text] [Related]
10. Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials.
Luitz MP; Zacharias M
J Chem Inf Model; 2014 Jun; 54(6):1669-75. PubMed ID: 24855894
[TBL] [Abstract][Full Text] [Related]
11. Water, shape recognition, salt bridges, and cation-pi interactions differentiate peptide recognition of the HIV rev-responsive element.
Michael LA; Chenault JA; Miller BR; Knolhoff AM; Nagan MC
J Mol Biol; 2009 Sep; 392(3):774-86. PubMed ID: 19631217
[TBL] [Abstract][Full Text] [Related]
12. A new method for evaluating the specificity of indirect readout in protein-DNA recognition.
Yamasaki S; Terada T; Kono H; Shimizu K; Sarai A
Nucleic Acids Res; 2012 Sep; 40(17):e129. PubMed ID: 22618872
[TBL] [Abstract][Full Text] [Related]
13. Alternative binding modes of proline-rich peptides binding to the GYF domain.
Gu W; Kofler M; Antes I; Freund C; Helms V
Biochemistry; 2005 May; 44(17):6404-15. PubMed ID: 15850374
[TBL] [Abstract][Full Text] [Related]
14. Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition.
Araúzo-Bravo MJ; Fujii S; Kono H; Ahmad S; Sarai A
J Am Chem Soc; 2005 Nov; 127(46):16074-89. PubMed ID: 16287294
[TBL] [Abstract][Full Text] [Related]
15. Characterization by NMR and molecular modeling of the binding of polyisoprenols and polyisoprenyl recognition sequence peptides: 3D structure of the complexes reveals sites of specific interactions.
Zhou GP; Troy FA
Glycobiology; 2003 Feb; 13(2):51-71. PubMed ID: 12626407
[TBL] [Abstract][Full Text] [Related]
16. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures.
Larson SM; Davidson AR
Protein Sci; 2000 Nov; 9(11):2170-80. PubMed ID: 11152127
[TBL] [Abstract][Full Text] [Related]
17. Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.
You W; Huang YM; Kizhake S; Natarajan A; Chang CE
PLoS Comput Biol; 2016 Aug; 12(8):e1005057. PubMed ID: 27560145
[TBL] [Abstract][Full Text] [Related]
18. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.
London N; Raveh B; Schueler-Furman O
Curr Opin Struct Biol; 2013 Dec; 23(6):894-902. PubMed ID: 24138780
[TBL] [Abstract][Full Text] [Related]
19. Protein design to understand peptide ligand recognition by tetratricopeptide repeat proteins.
Cortajarena AL; Kajander T; Pan W; Cocco MJ; Regan L
Protein Eng Des Sel; 2004 Apr; 17(4):399-409. PubMed ID: 15166314
[TBL] [Abstract][Full Text] [Related]
20. Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain.
He P; Wu W; Wang HD; Liao KL; Zhang W; Lv FL; Yang K
J Theor Biol; 2014 Jan; 340():30-7. PubMed ID: 24021866
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]