167 related articles for article (PubMed ID: 15725015)
21. Funnel metadynamics as accurate binding free-energy method.
Limongelli V; Bonomi M; Parrinello M
Proc Natl Acad Sci U S A; 2013 Apr; 110(16):6358-63. PubMed ID: 23553839
[TBL] [Abstract][Full Text] [Related]
22. Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex.
Zhang DW; Xiang Y; Gao AM; Zhang JZ
J Chem Phys; 2004 Jan; 120(3):1145-8. PubMed ID: 15268233
[TBL] [Abstract][Full Text] [Related]
23. Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.
Dickson A; Lotz SD
Biophys J; 2017 Feb; 112(4):620-629. PubMed ID: 28256222
[TBL] [Abstract][Full Text] [Related]
24. Molecular dynamics simulation of the docking of substrates to proteins.
Di Nola A; Roccatano D; Berendsen HJ
Proteins; 1994 Jul; 19(3):174-82. PubMed ID: 7937732
[TBL] [Abstract][Full Text] [Related]
25. Calculation of protein-ligand binding free energy by using a polarizable potential.
Jiao D; Golubkov PA; Darden TA; Ren P
Proc Natl Acad Sci U S A; 2008 Apr; 105(17):6290-5. PubMed ID: 18427113
[TBL] [Abstract][Full Text] [Related]
26. Crystal structure reveals basis for the inhibitor resistance of human brain trypsin.
Katona G; Berglund GI; Hajdu J; Gráf L; Szilágyi L
J Mol Biol; 2002 Feb; 315(5):1209-18. PubMed ID: 11827488
[TBL] [Abstract][Full Text] [Related]
27. Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
Schiebel J; Gaspari R; Wulsdorf T; Ngo K; Sohn C; Schrader TE; Cavalli A; Ostermann A; Heine A; Klebe G
Nat Commun; 2018 Sep; 9(1):3559. PubMed ID: 30177695
[TBL] [Abstract][Full Text] [Related]
28. Loop flexibility and solvent dynamics as determinants for the selective inhibition of cyclin-dependent kinase 4: comparative molecular dynamics simulation studies of CDK2 and CDK4.
Park H; Yeom MS; Lee S
Chembiochem; 2004 Dec; 5(12):1662-72. PubMed ID: 15505811
[TBL] [Abstract][Full Text] [Related]
29. How Effectively Can Adaptive Sampling Methods Capture Spontaneous Ligand Binding?
Betz RM; Dror RO
J Chem Theory Comput; 2019 Mar; 15(3):2053-2063. PubMed ID: 30645108
[TBL] [Abstract][Full Text] [Related]
30. Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.
Wang J; Dixon R; Kollman PA
Proteins; 1999 Jan; 34(1):69-81. PubMed ID: 10336384
[TBL] [Abstract][Full Text] [Related]
31. SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy.
Wu G; Vieth M
J Med Chem; 2004 Jun; 47(12):3142-8. PubMed ID: 15163194
[TBL] [Abstract][Full Text] [Related]
32. Water access and ligand dissociation at the binding site of proteins.
Yonetani Y
J Chem Phys; 2018 Nov; 149(17):175102. PubMed ID: 30408972
[TBL] [Abstract][Full Text] [Related]
33. Molecular docking of balanol to dynamics snapshots of protein kinase A.
Wong CF; Kua J; Zhang Y; Straatsma TP; McCammon JA
Proteins; 2005 Dec; 61(4):850-8. PubMed ID: 16245317
[TBL] [Abstract][Full Text] [Related]
34. Analysis of CDK2 active-site hydration: a method to design new inhibitors.
Kríz Z; Otyepka M; Bártová I; Koca J
Proteins; 2004 May; 55(2):258-74. PubMed ID: 15048820
[TBL] [Abstract][Full Text] [Related]
35. An improved
Calle LP; Espinosa JF
Magn Reson Chem; 2017 Apr; 55(4):355-358. PubMed ID: 27661784
[No Abstract] [Full Text] [Related]
36. Zymogen activation: effect of peptides sequentially related to the bovine beta-trypsin N-terminus on Kazal inhibitor and benzamidine binding to bovine trypsinogen.
Ascenzi P; Coletta M; Amiconi G; Bolognesi M; Guarneri M; Menegatti E
J Mol Recognit; 1988 Jun; 1(3):130-7. PubMed ID: 3273224
[TBL] [Abstract][Full Text] [Related]
37. Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase.
Renatus M; Bode W; Huber R; Stürzebecher J; Stubbs MT
J Med Chem; 1998 Dec; 41(27):5445-56. PubMed ID: 9876114
[TBL] [Abstract][Full Text] [Related]
38. A plausible identification of the secondary binding site in trypsin and trypsinogen.
Andrade MH; Silva E; Mares-Guia M
Braz J Med Biol Res; 1990; 23(12):1223-31. PubMed ID: 2136554
[TBL] [Abstract][Full Text] [Related]
39. Reranking docking poses using molecular simulations and approximate free energy methods.
Lauro G; Ferruz N; Fulle S; Harvey MJ; Finn PW; De Fabritiis G
J Chem Inf Model; 2014 Aug; 54(8):2185-9. PubMed ID: 25046765
[TBL] [Abstract][Full Text] [Related]
40. Performance of 3D-database molecular docking studies into homology models.
Oshiro C; Bradley EK; Eksterowicz J; Evensen E; Lamb ML; Lanctot JK; Putta S; Stanton R; Grootenhuis PD
J Med Chem; 2004 Jan; 47(3):764-7. PubMed ID: 14736258
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]