153 related articles for article (PubMed ID: 24623614)
1. Protein side-chain modeling with a protein-dependent optimized rotamer library.
Francis-Lyon P; Koehl P
Proteins; 2014 Sep; 82(9):2000-17. PubMed ID: 24623614
[TBL] [Abstract][Full Text] [Related]
2. Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.
Mendes J; Nagarajaram HA; Soares CM; Blundell TL; Carrondo MA
Biopolymers; 2001 Aug; 59(2):72-86. PubMed ID: 11373721
[TBL] [Abstract][Full Text] [Related]
3. Docking and scoring with alternative side-chain conformations.
Hartmann C; Antes I; Lengauer T
Proteins; 2009 Feb; 74(3):712-26. PubMed ID: 18704939
[TBL] [Abstract][Full Text] [Related]
4. IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
Hartmann C; Antes I; Lengauer T
Protein Sci; 2007 Jul; 16(7):1294-307. PubMed ID: 17567749
[TBL] [Abstract][Full Text] [Related]
5. Design of a rotamer library for coarse-grained models in protein-folding simulations.
Larriva M; Rey A
J Chem Inf Model; 2014 Jan; 54(1):302-13. PubMed ID: 24354725
[TBL] [Abstract][Full Text] [Related]
6. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.
Nagata K; Randall A; Baldi P
Proteins; 2012 Jan; 80(1):142-53. PubMed ID: 22072531
[TBL] [Abstract][Full Text] [Related]
7. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
Bower MJ; Cohen FE; Dunbrack RL
J Mol Biol; 1997 Apr; 267(5):1268-82. PubMed ID: 9150411
[TBL] [Abstract][Full Text] [Related]
8. Side-chain modeling with an optimized scoring function.
Liang S; Grishin NV
Protein Sci; 2002 Feb; 11(2):322-31. PubMed ID: 11790842
[TBL] [Abstract][Full Text] [Related]
9. A protein-dependent side-chain rotamer library.
Bhuyan MS; Gao X
BMC Bioinformatics; 2011 Dec; 12 Suppl 14(Suppl 14):S10. PubMed ID: 22373394
[TBL] [Abstract][Full Text] [Related]
10. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction.
Mendes J; Soares CM; Carrondo MA
Biopolymers; 1999 Aug; 50(2):111-31. PubMed ID: 10380336
[TBL] [Abstract][Full Text] [Related]
11. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search.
Wilson C; Gregoret LM; Agard DA
J Mol Biol; 1993 Feb; 229(4):996-1006. PubMed ID: 8445659
[TBL] [Abstract][Full Text] [Related]
12. An energy-based conformer library for side chain optimization: improved prediction and adjustable sampling.
Subramaniam S; Senes A
Proteins; 2012 Aug; 80(9):2218-34. PubMed ID: 22576292
[TBL] [Abstract][Full Text] [Related]
13. GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations.
Yang JM; Tsai CH; Hwang MJ; Tsai HK; Hwang JK; Kao CY
Protein Sci; 2002 Aug; 11(8):1897-907. PubMed ID: 12142444
[TBL] [Abstract][Full Text] [Related]
14. Solving and analyzing side-chain positioning problems using linear and integer programming.
Kingsford CL; Chazelle B; Singh M
Bioinformatics; 2005 Apr; 21(7):1028-36. PubMed ID: 15546935
[TBL] [Abstract][Full Text] [Related]
15. Improved prediction of protein side-chain conformations with SCWRL4.
Krivov GG; Shapovalov MV; Dunbrack RL
Proteins; 2009 Dec; 77(4):778-95. PubMed ID: 19603484
[TBL] [Abstract][Full Text] [Related]
16. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
Taylor RD; Jewsbury PJ; Essex JW
J Comput Chem; 2003 Oct; 24(13):1637-56. PubMed ID: 12926007
[TBL] [Abstract][Full Text] [Related]
17. Extending the accuracy limits of prediction for side-chain conformations.
Xiang Z; Honig B
J Mol Biol; 2001 Aug; 311(2):421-30. PubMed ID: 11478870
[TBL] [Abstract][Full Text] [Related]
18. The energetics of off-rotamer protein side-chain conformations.
Petrella RJ; Karplus M
J Mol Biol; 2001 Oct; 312(5):1161-75. PubMed ID: 11580256
[TBL] [Abstract][Full Text] [Related]
19. Improved side-chain modeling for protein-protein docking.
Wang C; Schueler-Furman O; Baker D
Protein Sci; 2005 May; 14(5):1328-39. PubMed ID: 15802647
[TBL] [Abstract][Full Text] [Related]
20. Structure refinement of protein model decoys requires accurate side-chain placement.
Olson MA; Lee MS
Proteins; 2013 Mar; 81(3):469-78. PubMed ID: 23070940
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]