279 related articles for article (PubMed ID: 33599485)
1. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.
Smith RD; Carlson HA
J Chem Inf Model; 2021 Mar; 61(3):1287-1299. PubMed ID: 33599485
[TBL] [Abstract][Full Text] [Related]
2. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems.
Ghanakota P; Carlson HA
J Phys Chem B; 2016 Aug; 120(33):8685-95. PubMed ID: 27258368
[TBL] [Abstract][Full Text] [Related]
3. MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations.
Graham SE; Leja N; Carlson HA
J Chem Inf Model; 2018 Jul; 58(7):1426-1433. PubMed ID: 29905479
[TBL] [Abstract][Full Text] [Related]
4. Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations.
Ghanakota P; DasGupta D; Carlson HA
J Chem Inf Model; 2019 May; 59(5):2035-2045. PubMed ID: 31017411
[TBL] [Abstract][Full Text] [Related]
5. Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes.
Feng Y; Gong C; Zhu J; Liu G; Tang Y; Li W
J Chem Inf Model; 2024 Apr; 64(8):3451-3464. PubMed ID: 38593186
[TBL] [Abstract][Full Text] [Related]
6. Application of Mixed-Solvent Molecular Dynamics Simulations for Prediction of Allosteric Sites on G Protein-Coupled Receptors.
Chan WKB; Carlson HA; Traynor JR
Mol Pharmacol; 2023 May; 103(5):274-285. PubMed ID: 36868791
[TBL] [Abstract][Full Text] [Related]
7. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.
Frembgen-Kesner T; Elcock AH
J Mol Biol; 2006 May; 359(1):202-14. PubMed ID: 16616932
[TBL] [Abstract][Full Text] [Related]
8. Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.
Graham SE; Smith RD; Carlson HA
J Chem Inf Model; 2018 Feb; 58(2):305-314. PubMed ID: 29286658
[TBL] [Abstract][Full Text] [Related]
9. Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.
Lexa KW; Goh GB; Carlson HA
J Chem Inf Model; 2014 Aug; 54(8):2190-9. PubMed ID: 25058662
[TBL] [Abstract][Full Text] [Related]
10. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites.
Tze-Yang Ng J; Tan YS
J Chem Theory Comput; 2022 Mar; 18(3):1969-1981. PubMed ID: 35175753
[TBL] [Abstract][Full Text] [Related]
11. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth.
Lal Gupta P; Carlson HA
J Chem Theory Comput; 2022 Jun; 18(6):3829-3844. PubMed ID: 35533286
[TBL] [Abstract][Full Text] [Related]
12. Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case.
Ung PM; Ghanakota P; Graham SE; Lexa KW; Carlson HA
Biopolymers; 2016 Jan; 105(1):21-34. PubMed ID: 26385317
[TBL] [Abstract][Full Text] [Related]
13. Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.
Kimura SR; Hu HP; Ruvinsky AM; Sherman W; Favia AD
J Chem Inf Model; 2017 Jun; 57(6):1388-1401. PubMed ID: 28537745
[TBL] [Abstract][Full Text] [Related]
14. Exploring the structural origins of cryptic sites on proteins.
Beglov D; Hall DR; Wakefield AE; Luo L; Allen KN; Kozakov D; Whitty A; Vajda S
Proc Natl Acad Sci U S A; 2018 Apr; 115(15):E3416-E3425. PubMed ID: 29581267
[TBL] [Abstract][Full Text] [Related]
15. Identifying Potential Ligand Binding Sites on Glycogen Synthase Kinase 3 Using Atomistic Cosolvent Simulations.
DasGupta D; Mehrani R; Carlson HA; Sharma S
ACS Appl Bio Mater; 2024 Feb; 7(2):588-595. PubMed ID: 37141501
[TBL] [Abstract][Full Text] [Related]
16. Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches.
Bansia H; Mahanta P; Yennawar NH; Ramakumar S
J Chem Inf Model; 2021 Mar; 61(3):1322-1333. PubMed ID: 33570386
[TBL] [Abstract][Full Text] [Related]
17. Structure-Based Analysis of Cryptic-Site Opening.
Sun Z; Wakefield AE; Kolossvary I; Beglov D; Vajda S
Structure; 2020 Feb; 28(2):223-235.e2. PubMed ID: 31810712
[TBL] [Abstract][Full Text] [Related]
18. Improving protocols for protein mapping through proper comparison to crystallography data.
Lexa KW; Carlson HA
J Chem Inf Model; 2013 Feb; 53(2):391-402. PubMed ID: 23327200
[TBL] [Abstract][Full Text] [Related]
19. PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations.
Martinez-Rosell G; Lovera S; Sands ZA; De Fabritiis G
J Chem Inf Model; 2020 Apr; 60(4):2314-2324. PubMed ID: 32175736
[TBL] [Abstract][Full Text] [Related]
20. Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design.
Schmidt D; Boehm M; McClendon CL; Torella R; Gohlke H
J Chem Theory Comput; 2019 May; 15(5):3331-3343. PubMed ID: 30998331
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]