157 related articles for article (PubMed ID: 9263850)
1. An automated method for predicting the positions of hydrogen-bonding atoms in binding sites.
Mills JE; Perkins TD; Dean PM
J Comput Aided Mol Des; 1997 May; 11(3):229-42. PubMed ID: 9263850
[TBL] [Abstract][Full Text] [Related]
2. SLATE: a method for the superposition of flexible ligands.
Mills JE; de Esch IJ; Perkins TD; Dean PM
J Comput Aided Mol Des; 2001 Jan; 15(1):81-96. PubMed ID: 11217921
[TBL] [Abstract][Full Text] [Related]
3. Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design.
Bohacek RS; McMartin C
J Med Chem; 1992 May; 35(10):1671-84. PubMed ID: 1588550
[TBL] [Abstract][Full Text] [Related]
4. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase.
Murray CW; Baxter CA; Frenkel AD
J Comput Aided Mol Des; 1999 Nov; 13(6):547-62. PubMed ID: 10584214
[TBL] [Abstract][Full Text] [Related]
5. AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms.
Ravindranath PA; Sanner MF
Bioinformatics; 2016 Oct; 32(20):3142-3149. PubMed ID: 27354702
[TBL] [Abstract][Full Text] [Related]
6. Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.
Brandstetter H; Turk D; Hoeffken HW; Grosse D; Stürzebecher J; Martin PD; Edwards BF; Bode W
J Mol Biol; 1992 Aug; 226(4):1085-99. PubMed ID: 1518046
[TBL] [Abstract][Full Text] [Related]
7. Time-efficient flexible superposition of medium-sized molecules.
Lemmen C; Lengauer T
J Comput Aided Mol Des; 1997 Jul; 11(4):357-68. PubMed ID: 9334902
[TBL] [Abstract][Full Text] [Related]
8. Molecular surface-volume and property matching to superpose flexible dissimilar molecules.
Perkins TD; Mills JE; Dean PM
J Comput Aided Mol Des; 1995 Dec; 9(6):479-90. PubMed ID: 8789190
[TBL] [Abstract][Full Text] [Related]
9. An example of a protein ligand found by database mining: description of the docking method and its verification by a 2.3 A X-ray structure of a thrombin-ligand complex.
Burkhard P; Taylor P; Walkinshaw MD
J Mol Biol; 1998 Mar; 277(2):449-66. PubMed ID: 9514757
[TBL] [Abstract][Full Text] [Related]
10. Automated site-directed drug design: the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces.
Danziger DJ; Dean PM
Proc R Soc Lond B Biol Sci; 1989 Mar; 236(1283):115-24. PubMed ID: 2565576
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. An electronic environment and contact direction sensitive scoring function for predicting affinities of protein-ligand complexes in Contour(®).
Lindblom PR; Wu G; Liu Z; Jim KC; Baldwin JJ; Gregg RE; Claremon DA; Singh SB
J Mol Graph Model; 2014 Sep; 53():118-127. PubMed ID: 25123650
[TBL] [Abstract][Full Text] [Related]
13. Identification of substrate binding sites in enzymes by computational solvent mapping.
Silberstein M; Dennis S; Brown L; Kortvelyesi T; Clodfelter K; Vajda S
J Mol Biol; 2003 Oct; 332(5):1095-113. PubMed ID: 14499612
[TBL] [Abstract][Full Text] [Related]
14. Experimental and computational active site mapping as a starting point to fragment-based lead discovery.
Behnen J; Köster H; Neudert G; Craan T; Heine A; Klebe G
ChemMedChem; 2012 Feb; 7(2):248-61. PubMed ID: 22213702
[TBL] [Abstract][Full Text] [Related]
15. Different approaches toward an automatic structural alignment of drug molecules: applications to sterol mimics, thrombin and thermolysin inhibitors.
Klebe G; Mietzner T; Weber F
J Comput Aided Mol Des; 1994 Dec; 8(6):751-78. PubMed ID: 7738608
[TBL] [Abstract][Full Text] [Related]
16. Differences in hydropathic properties of ligand binding at four independent sites in wheat germ agglutinin-oligosaccharide crystal complexes.
Wright CS; Kellogg GE
Protein Sci; 1996 Aug; 5(8):1466-76. PubMed ID: 8844838
[TBL] [Abstract][Full Text] [Related]
17. A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site.
Katz BA; Elrod K; Luong C; Rice MJ; Mackman RL; Sprengeler PA; Spencer J; Hataye J; Janc J; Link J; Litvak J; Rai R; Rice K; Sideris S; Verner E; Young W
J Mol Biol; 2001 Apr; 307(5):1451-86. PubMed ID: 11292354
[TBL] [Abstract][Full Text] [Related]
18. Computational mapping identifies the binding sites of organic solvents on proteins.
Dennis S; Kortvelyesi T; Vajda S
Proc Natl Acad Sci U S A; 2002 Apr; 99(7):4290-5. PubMed ID: 11904374
[TBL] [Abstract][Full Text] [Related]
19. Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.
Raschka S; Wolf AJ; Bemister-Buffington J; Kuhn LA
J Comput Aided Mol Des; 2018 Apr; 32(4):511-528. PubMed ID: 29435780
[TBL] [Abstract][Full Text] [Related]
20. Experimental and computational mapping of the binding surface of a crystalline protein.
English AC; Groom CR; Hubbard RE
Protein Eng; 2001 Jan; 14(1):47-59. PubMed ID: 11287678
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]