138 related articles for article (PubMed ID: 29018806)
1. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.
Panel N; Sun YJ; Fuentes EJ; Simonson T
Front Mol Biosci; 2017; 4():65. PubMed ID: 29018806
[TBL] [Abstract][Full Text] [Related]
2. The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion.
Shepherd TR; Klaus SM; Liu X; Ramaswamy S; DeMali KA; Fuentes EJ
J Mol Biol; 2010 May; 398(5):730-46. PubMed ID: 20361982
[TBL] [Abstract][Full Text] [Related]
3. Computational Design of PDZ-Peptide Binding.
Panel N; Villa F; Opuu V; Mignon D; Simonson T
Methods Mol Biol; 2021; 2256():237-255. PubMed ID: 34014526
[TBL] [Abstract][Full Text] [Related]
4. Structural and thermodynamic analysis of PDZ-ligand interactions.
Shepherd TR; Fuentes EJ
Methods Enzymol; 2011; 488():81-100. PubMed ID: 21195225
[TBL] [Abstract][Full Text] [Related]
5. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.
Hou T; Zhang W; Case DA; Wang W
J Mol Biol; 2008 Feb; 376(4):1201-14. PubMed ID: 18206907
[TBL] [Abstract][Full Text] [Related]
6. Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.
Panel N; Villa F; Fuentes EJ; Simonson T
Biophys J; 2018 Mar; 114(5):1091-1102. PubMed ID: 29539396
[TBL] [Abstract][Full Text] [Related]
7. Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors.
Zoete V; Michielin O; Karplus M
J Comput Aided Mol Des; 2003 Dec; 17(12):861-80. PubMed ID: 15124934
[TBL] [Abstract][Full Text] [Related]
8. Structure-based identification of CaMKIIα-interacting MUPP1 PDZ domains and rational design of peptide ligands to target such interaction in human fertilization.
Zhang YL; Han ZF; Sun YP
Amino Acids; 2016 Jun; 48(6):1509-21. PubMed ID: 26984442
[TBL] [Abstract][Full Text] [Related]
9. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
Genheden S; Ryde U
Proteins; 2012 May; 80(5):1326-42. PubMed ID: 22274991
[TBL] [Abstract][Full Text] [Related]
10. Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.
Kasper P; Christen P; Gehring H
Proteins; 2000 Aug; 40(2):185-92. PubMed ID: 10842335
[TBL] [Abstract][Full Text] [Related]
11. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
Sham YY; Chu ZT; Tao H; Warshel A
Proteins; 2000 Jun; 39(4):393-407. PubMed ID: 10813821
[TBL] [Abstract][Full Text] [Related]
12. Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding.
Mignon D; Panel N; Chen X; Fuentes EJ; Simonson T
J Chem Theory Comput; 2017 May; 13(5):2271-2289. PubMed ID: 28394603
[TBL] [Abstract][Full Text] [Related]
13. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.
Miranda WE; Noskov SY; Valiente PA
J Chem Inf Model; 2015 Sep; 55(9):1867-77. PubMed ID: 26180998
[TBL] [Abstract][Full Text] [Related]
14. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
van Lipzig MM; ter Laak AM; Jongejan A; Vermeulen NP; Wamelink M; Geerke D; Meerman JH
J Med Chem; 2004 Feb; 47(4):1018-30. PubMed ID: 14761204
[TBL] [Abstract][Full Text] [Related]
15. Continuum solvation models in the linear interaction energy method.
Carlsson J; Andér M; Nervall M; Aqvist J
J Phys Chem B; 2006 Jun; 110(24):12034-41. PubMed ID: 16800513
[TBL] [Abstract][Full Text] [Related]
16. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
Aleksandrov A; Lin FY; Roux B; MacKerell AD
J Comput Chem; 2018 Aug; 39(22):1707-1719. PubMed ID: 29737546
[TBL] [Abstract][Full Text] [Related]
17. Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses.
Tian F; Lv Y; Zhou P; Yang L
J Comput Aided Mol Des; 2011 Oct; 25(10):947-58. PubMed ID: 21964565
[TBL] [Abstract][Full Text] [Related]
18. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
Archontis G; Simonson T; Karplus M
J Mol Biol; 2001 Feb; 306(2):307-27. PubMed ID: 11237602
[TBL] [Abstract][Full Text] [Related]
19. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
Wang W; Wang J; Kollman PA
Proteins; 1999 Feb; 34(3):395-402. PubMed ID: 10024025
[TBL] [Abstract][Full Text] [Related]
20. Single-amino acid substitutions alter the specificity and affinity of PDZ domains for their ligands.
Gee SH; Quenneville S; Lombardo CR; Chabot J
Biochemistry; 2000 Nov; 39(47):14638-46. PubMed ID: 11087420
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
