267 related articles for article (PubMed ID: 22183545)
1. Linear interaction energy: method and applications in drug design.
Gutiérrez-de-Terán H; Aqvist J
Methods Mol Biol; 2012; 819():305-23. PubMed ID: 22183545
[TBL] [Abstract][Full Text] [Related]
2. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
Woo HJ
Methods Mol Biol; 2008; 443():109-20. PubMed ID: 18446284
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.
Estrada T; Zhang B; Cicotti P; Armen RS; Taufer M
Comput Biol Med; 2012 Jul; 42(7):758-71. PubMed ID: 22658682
[TBL] [Abstract][Full Text] [Related]
5. The solvated interaction energy method for scoring binding affinities.
Sulea T; Purisima EO
Methods Mol Biol; 2012; 819():295-303. PubMed ID: 22183544
[TBL] [Abstract][Full Text] [Related]
6. Molecular recognition of RNA: challenges for modelling interactions and plasticity.
Fulle S; Gohlke H
J Mol Recognit; 2010; 23(2):220-31. PubMed ID: 19941322
[TBL] [Abstract][Full Text] [Related]
7. Accelerated molecular dynamics in computational drug design.
Wereszczynski J; McCammon JA
Methods Mol Biol; 2012; 819():515-24. PubMed ID: 22183555
[TBL] [Abstract][Full Text] [Related]
8. Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach.
Oostenbrink C
J Comput Chem; 2009 Jan; 30(2):212-21. PubMed ID: 18785242
[TBL] [Abstract][Full Text] [Related]
9. Incorporating receptor flexibility in the molecular design of protein interfaces.
Li L; Liang S; Pilcher MM; Meroueh SO
Protein Eng Des Sel; 2009 Sep; 22(9):575-86. PubMed ID: 19643976
[TBL] [Abstract][Full Text] [Related]
10. Best practices in free energy calculations for drug design.
Shirts MR
Methods Mol Biol; 2012; 819():425-67. PubMed ID: 22183551
[TBL] [Abstract][Full Text] [Related]
11. Molecular modeling of hydration in drug design.
Mancera RL
Curr Opin Drug Discov Devel; 2007 May; 10(3):275-80. PubMed ID: 17554853
[TBL] [Abstract][Full Text] [Related]
12. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.
Lawrenz M; Baron R; Wang Y; McCammon JA
Methods Mol Biol; 2012; 819():469-86. PubMed ID: 22183552
[TBL] [Abstract][Full Text] [Related]
13. Prediction of protein-ligand binding affinities using multiple instance learning.
Teramoto R; Kashima H
J Mol Graph Model; 2010 Nov; 29(3):492-7. PubMed ID: 20965757
[TBL] [Abstract][Full Text] [Related]
14. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.
Liu J; He X; Zhang JZ
J Chem Inf Model; 2013 Jun; 53(6):1306-14. PubMed ID: 23651068
[TBL] [Abstract][Full Text] [Related]
15. Accuracy assessment and automation of free energy calculations for drug design.
Christ CD; Fox T
J Chem Inf Model; 2014 Jan; 54(1):108-20. PubMed ID: 24256082
[TBL] [Abstract][Full Text] [Related]
16. Physics-based methods for studying protein-ligand interactions.
Huang N; Jacobson MP
Curr Opin Drug Discov Devel; 2007 May; 10(3):325-31. PubMed ID: 17554859
[TBL] [Abstract][Full Text] [Related]
17. Molecular Dynamics as a Tool for Virtual Ligand Screening.
Menchon G; Maveyraud L; Czaplicki G
Methods Mol Biol; 2018; 1762():145-178. PubMed ID: 29594772
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations.
Geroult S; Hooda M; Virdee S; Waksman G
Chem Biol Drug Des; 2007 Aug; 70(2):87-99. PubMed ID: 17683370
[TBL] [Abstract][Full Text] [Related]
20. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.
Woods CJ; Malaisree M; Hannongbua S; Mulholland AJ
J Chem Phys; 2011 Feb; 134(5):054114. PubMed ID: 21303099
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]