170 related articles for article (PubMed ID: 23376613)
1. AutoMap: a tool for analyzing protein-ligand recognition using multiple ligand binding modes.
Agostino M; Mancera RL; Ramsland PA; Yuriev E
J Mol Graph Model; 2013 Mar; 40():80-90. PubMed ID: 23376613
[TBL] [Abstract][Full Text] [Related]
2. Antibody-Carbohydrate Recognition from Docked Ensembles Using the AutoMap Procedure.
Dingjan T; Agostino M; Ramsland PA; Yuriev E
Methods Mol Biol; 2015; 1331():41-55. PubMed ID: 26169734
[TBL] [Abstract][Full Text] [Related]
3. Rational automatic search method for stable docking models of protein and ligand.
Mizutani MY; Tomioka N; Itai A
J Mol Biol; 1994 Oct; 243(2):310-26. PubMed ID: 7932757
[TBL] [Abstract][Full Text] [Related]
4. NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
Asensio JL; Siebert HC; von Der Lieth CW; Laynez J; Bruix M; Soedjanaamadja UM; Beintema JJ; Cañada FJ; Gabius HJ; Jiménez-Barbero J
Proteins; 2000 Aug; 40(2):218-36. PubMed ID: 10842338
[TBL] [Abstract][Full Text] [Related]
5. Solvent structure improves docking prediction in lectin-carbohydrate complexes.
Gauto DF; Petruk AA; Modenutti CP; Blanco JI; Di Lella S; Martí MA
Glycobiology; 2013 Feb; 23(2):241-58. PubMed ID: 23089616
[TBL] [Abstract][Full Text] [Related]
6. Development and application of site mapping methods for the design of glycosaminoglycans.
Agostino M; Gandhi NS; Mancera RL
Glycobiology; 2014 Sep; 24(9):840-51. PubMed ID: 24859723
[TBL] [Abstract][Full Text] [Related]
7. Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures.
Agostino M; Jene C; Boyle T; Ramsland PA; Yuriev E
J Chem Inf Model; 2009 Dec; 49(12):2749-60. PubMed ID: 19994843
[TBL] [Abstract][Full Text] [Related]
8. Phage display screening against a set of targets to establish peptide-based sugar mimetics and molecular docking to predict binding site.
Yu L; Yu PS; Yee Yen Mui E; McKelvie JC; Pham TP; Yap YW; Wong WQ; Wu J; Deng W; Orner BP
Bioorg Med Chem; 2009 Jul; 17(13):4825-32. PubMed ID: 19447041
[TBL] [Abstract][Full Text] [Related]
9. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.
Huang SY; Zou X
Proteins; 2007 Feb; 66(2):399-421. PubMed ID: 17096427
[TBL] [Abstract][Full Text] [Related]
10. Docking ligands onto binding site representations derived from proteins built by homology modelling.
Schafferhans A; Klebe G
J Mol Biol; 2001 Mar; 307(1):407-27. PubMed ID: 11243828
[TBL] [Abstract][Full Text] [Related]
11. Ph4Dock: pharmacophore-based protein-ligand docking.
Goto J; Kataoka R; Hirayama N
J Med Chem; 2004 Dec; 47(27):6804-11. PubMed ID: 15615529
[TBL] [Abstract][Full Text] [Related]
12. SuperStar: improved knowledge-based interaction fields for protein binding sites.
Verdonk ML; Cole JC; Watson P; Gillet V; Willett P
J Mol Biol; 2001 Mar; 307(3):841-59. PubMed ID: 11273705
[TBL] [Abstract][Full Text] [Related]
13. Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions.
Zheng M; Xiong B; Luo C; Li S; Liu X; Shen Q; Li J; Zhu W; Luo X; Jiang H
J Chem Inf Model; 2011 Nov; 51(11):2994-3004. PubMed ID: 21999432
[TBL] [Abstract][Full Text] [Related]
14. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.
Li H; Li C
J Comput Chem; 2010 Jul; 31(10):2014-22. PubMed ID: 20166125
[TBL] [Abstract][Full Text] [Related]
15. [Computer drug design based on analysis of a target macromolecule structure. I. Search and description of a ligand binding site in a target molecule].
Ivanov AS; Dubanov AV; Skvortsov VS; Archakov AI
Vopr Med Khim; 2002; 48(3):304-15. PubMed ID: 12243090
[TBL] [Abstract][Full Text] [Related]
16. Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
Virtanen SI; Pentikäinen OT
J Chem Inf Model; 2010 Jun; 50(6):1005-11. PubMed ID: 20504004
[TBL] [Abstract][Full Text] [Related]
17. FlexE: efficient molecular docking considering protein structure variations.
Claussen H; Buning C; Rarey M; Lengauer T
J Mol Biol; 2001 Apr; 308(2):377-95. PubMed ID: 11327774
[TBL] [Abstract][Full Text] [Related]
18. Peptide inhibitors of xenoreactive antibodies mimic the interaction profile of the native carbohydrate antigens.
Agostino M; Sandrin MS; Thompson PE; Ramsland PA; Yuriev E
Biopolymers; 2011; 96(2):193-206. PubMed ID: 20564023
[TBL] [Abstract][Full Text] [Related]
19. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.
Floriano WB; Vaidehi N; Zamanakos G; Goddard WA
J Med Chem; 2004 Jan; 47(1):56-71. PubMed ID: 14695820
[TBL] [Abstract][Full Text] [Related]
20. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.
Laurie AT; Jackson RM
Bioinformatics; 2005 May; 21(9):1908-16. PubMed ID: 15701681
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
