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.
98 related articles for article (PubMed ID: 29023116)
1. Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm. Xiao X; Wang Y; Leonard JN; Hall CK J Chem Theory Comput; 2017 Nov; 13(11):5709-5720. PubMed ID: 29023116 [TBL] [Abstract][Full Text] [Related]
2. Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA. Xiao X; Hung ME; Leonard JN; Hall CK J Comput Chem; 2016 Oct; 37(27):2423-35. PubMed ID: 27487990 [TBL] [Abstract][Full Text] [Related]
3. Designing peptide sequences in flexible chain conformations to bind RNA: a search algorithm combining Monte Carlo, self-consistent mean field and concerted rotation techniques. Xiao X; Agris PF; Hall CK J Chem Theory Comput; 2015 Feb; 11(2):740-52. PubMed ID: 26579605 [TBL] [Abstract][Full Text] [Related]
4. Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success. Xiao X; Agris PF; Hall CK Proteins; 2016 May; 84(5):700-11. PubMed ID: 26914059 [TBL] [Abstract][Full Text] [Related]
5. Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics. Gladich I; Rodriguez A; Hong Enriquez RP; Guida F; Berti F; Laio A J Phys Chem B; 2015 Oct; 119(41):12963-9. PubMed ID: 26398715 [TBL] [Abstract][Full Text] [Related]
6. Enhanced conformational sampling using enveloping distribution sampling. Lin Z; van Gunsteren WF J Chem Phys; 2013 Oct; 139(14):144105. PubMed ID: 24116601 [TBL] [Abstract][Full Text] [Related]
7. Differential modes of recognition in N peptide-boxB complexes. Austin RJ; Xia T; Ren J; Takahashi TT; Roberts RW Biochemistry; 2003 Dec; 42(50):14957-67. PubMed ID: 14674772 [TBL] [Abstract][Full Text] [Related]
8. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Kannan S; Zacharias M Proteins; 2007 Feb; 66(3):697-706. PubMed ID: 17120231 [TBL] [Abstract][Full Text] [Related]
9. 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]
10. Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. Yu L; Barros SA; Sun C; Somani S J Chem Inf Model; 2023 Nov; 63(21):6863-6876. PubMed ID: 37903231 [TBL] [Abstract][Full Text] [Related]
11. Structural prediction of peptides binding to MHC class I molecules. Bui HH; Schiewe AJ; von Grafenstein H; Haworth IS Proteins; 2006 Apr; 63(1):43-52. PubMed ID: 16447245 [TBL] [Abstract][Full Text] [Related]
12. Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. de Groot BL; Amadei A; van Aalten DM; Berendsen HJ J Biomol Struct Dyn; 1996 Apr; 13(5):741-51. PubMed ID: 8723770 [TBL] [Abstract][Full Text] [Related]
13. Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution. Ghosh T; Garde S; García AE Biophys J; 2003 Nov; 85(5):3187-93. PubMed ID: 14581218 [TBL] [Abstract][Full Text] [Related]
14. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials. Hassan SA; Mehler EL; Zhang D; Weinstein H Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268 [TBL] [Abstract][Full Text] [Related]
15. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent. Peter EK; Shea JE; Pivkin IV Phys Chem Chem Phys; 2016 May; 18(18):13052-65. PubMed ID: 27111190 [TBL] [Abstract][Full Text] [Related]
16. Density-based clustering of small peptide conformations sampled from a molecular dynamics simulation. Kim M; Choi SH; Kim J; Choi K; Shin JM; Kang SK; Choi YJ; Jung DH J Chem Inf Model; 2009 Nov; 49(11):2528-36. PubMed ID: 19863092 [TBL] [Abstract][Full Text] [Related]
18. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft. Guvench O; Qu CK; MacKerell AD BMC Struct Biol; 2007 Mar; 7():14. PubMed ID: 17378938 [TBL] [Abstract][Full Text] [Related]
19. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model. Chen Y; Roux B J Chem Theory Comput; 2015 Aug; 11(8):3572-83. PubMed ID: 26574442 [TBL] [Abstract][Full Text] [Related]
20. Computational Modeling of Stapled Peptides toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics. Cornillie SP; Bruno BJ; Lim CS; Cheatham TE J Phys Chem B; 2018 Apr; 122(14):3864-3875. PubMed ID: 29519125 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]