588 related articles for article (PubMed ID: 17201676)
41. Theoretical Study of Protein-Ligand Interactions Using the Molecules-in-Molecules Fragmentation-Based Method.
Thapa B; Beckett D; Erickson J; Raghavachari K
J Chem Theory Comput; 2018 Oct; 14(10):5143-5155. PubMed ID: 30265003
[TBL] [Abstract][Full Text] [Related]
42. Evaluation of protein-ligand binding free energy focused on its entropic components.
Chiba S; Harano Y; Roth R; Kinoshita M; Sakurai M
J Comput Chem; 2012 Feb; 33(5):550-60. PubMed ID: 22162031
[TBL] [Abstract][Full Text] [Related]
43. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods.
Adekoya OA; Willassen NP; Sylte I
J Struct Biol; 2006 Feb; 153(2):129-44. PubMed ID: 16376106
[TBL] [Abstract][Full Text] [Related]
44. SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.
Eken Y; Almeida NMS; Wang C; Wilson AK
J Comput Aided Mol Des; 2021 Jan; 35(1):63-77. PubMed ID: 33150463
[TBL] [Abstract][Full Text] [Related]
45. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
Wang L; Wu Y; Deng Y; Kim B; Pierce L; Krilov G; Lupyan D; Robinson S; Dahlgren MK; Greenwood J; Romero DL; Masse C; Knight JL; Steinbrecher T; Beuming T; Damm W; Harder E; Sherman W; Brewer M; Wester R; Murcko M; Frye L; Farid R; Lin T; Mobley DL; Jorgensen WL; Berne BJ; Friesner RA; Abel R
J Am Chem Soc; 2015 Feb; 137(7):2695-703. PubMed ID: 25625324
[TBL] [Abstract][Full Text] [Related]
46. Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes.
Martin SF; Clements JH
Annu Rev Biochem; 2013; 82():267-93. PubMed ID: 23746256
[TBL] [Abstract][Full Text] [Related]
47. Some practical approaches to treating electrostatic polarization of proteins.
Ji C; Mei Y
Acc Chem Res; 2014 Sep; 47(9):2795-803. PubMed ID: 24883956
[TBL] [Abstract][Full Text] [Related]
48. Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique.
Mousseau N; Derreumaux P; Gilbert G
Phys Biol; 2005 Nov; 2(4):S101-7. PubMed ID: 16280615
[TBL] [Abstract][Full Text] [Related]
49. A theoretical analysis on hydration thermodynamics of proteins.
Imai T; Harano Y; Kinoshita M; Kovalenko A; Hirata F
J Chem Phys; 2006 Jul; 125(2):24911. PubMed ID: 16848615
[TBL] [Abstract][Full Text] [Related]
50. Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
Mulakala C; Viswanadhan VN
J Mol Graph Model; 2013 Nov; 46():41-51. PubMed ID: 24121518
[TBL] [Abstract][Full Text] [Related]
51. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.
Swanson JM; Henchman RH; McCammon JA
Biophys J; 2004 Jan; 86(1 Pt 1):67-74. PubMed ID: 14695250
[TBL] [Abstract][Full Text] [Related]
52. Computational study of ligand binding to protein receptors.
Wembridge P; Robinson H; Novak I
Bioorg Chem; 2008 Dec; 36(6):288-94. PubMed ID: 18801553
[TBL] [Abstract][Full Text] [Related]
53. Comparative assessment of QM-based and MM-based models for prediction of protein-ligand binding affinity trends.
Maier S; Thapa B; Erickson J; Raghavachari K
Phys Chem Chem Phys; 2022 Jun; 24(23):14525-14537. PubMed ID: 35661842
[TBL] [Abstract][Full Text] [Related]
54. Determination of the interfacial water content in protein-protein complexes from free energy simulations.
Monecke P; Borosch T; Brickmann J; Kast SM
Biophys J; 2006 Feb; 90(3):841-50. PubMed ID: 16284258
[TBL] [Abstract][Full Text] [Related]
55. Accurate Binding Free Energy Predictions in Fragment Optimization.
Steinbrecher TB; Dahlgren M; Cappel D; Lin T; Wang L; Krilov G; Abel R; Friesner R; Sherman W
J Chem Inf Model; 2015 Nov; 55(11):2411-20. PubMed ID: 26457994
[TBL] [Abstract][Full Text] [Related]
56. BRD4: quantum mechanical protein-ligand binding free energies using the full-protein DFT-based QM-PBSA method.
Gundelach L; Fox T; Tautermann CS; Skylaris CK
Phys Chem Chem Phys; 2022 Oct; 24(41):25240-25249. PubMed ID: 36222107
[TBL] [Abstract][Full Text] [Related]
57. Calculations of pH-dependent binding of proteins to biological membranes.
Mihajlovic M; Lazaridis T
J Phys Chem B; 2006 Feb; 110(7):3375-84. PubMed ID: 16494352
[TBL] [Abstract][Full Text] [Related]
58. Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.
Rifai EA; Ferrario V; Pleiss J; Geerke DP
J Chem Theory Comput; 2020 Feb; 16(2):1300-1310. PubMed ID: 31894691
[TBL] [Abstract][Full Text] [Related]
59. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.
Wang L; Deng Y; Wu Y; Kim B; LeBard DN; Wandschneider D; Beachy M; Friesner RA; Abel R
J Chem Theory Comput; 2017 Jan; 13(1):42-54. PubMed ID: 27933808
[TBL] [Abstract][Full Text] [Related]
60. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease.
Oehme DP; Brownlee RT; Wilson DJ
J Comput Chem; 2012 Dec; 33(32):2566-80. PubMed ID: 22915442
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
