371 related articles for article (PubMed ID: 30544890)
1. Solvents to Fragments to Drugs: MD Applications in Drug Design.
Defelipe LA; Arcon JP; Modenutti CP; Marti MA; Turjanski AG; Barril X
Molecules; 2018 Dec; 23(12):. PubMed ID: 30544890
[TBL] [Abstract][Full Text] [Related]
2. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.
Arcon JP; Defelipe LA; Modenutti CP; López ED; Alvarez-Garcia D; Barril X; Turjanski AG; Martí MA
J Chem Inf Model; 2017 Apr; 57(4):846-863. PubMed ID: 28318252
[TBL] [Abstract][Full Text] [Related]
3. Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix).
Alvarez-Garcia D; Schmidtke P; Cubero E; Barril X
Curr Drug Discov Technol; 2022; 19(2):62-68. PubMed ID: 34951392
[TBL] [Abstract][Full Text] [Related]
4. Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites.
Alvarez-Garcia D; Barril X
J Med Chem; 2014 Oct; 57(20):8530-9. PubMed ID: 25275946
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. Protein structure-based drug design: from docking to molecular dynamics.
Śledź P; Caflisch A
Curr Opin Struct Biol; 2018 Feb; 48():93-102. PubMed ID: 29149726
[TBL] [Abstract][Full Text] [Related]
7. Dynamic Docking: A Paradigm Shift in Computational Drug Discovery.
Gioia D; Bertazzo M; Recanatini M; Masetti M; Cavalli A
Molecules; 2017 Nov; 22(11):. PubMed ID: 29165360
[TBL] [Abstract][Full Text] [Related]
8. EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation.
Yanagisawa K; Moriwaki Y; Terada T; Shimizu K
J Chem Inf Model; 2021 Jun; 61(6):2744-2753. PubMed ID: 34061535
[TBL] [Abstract][Full Text] [Related]
9. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations.
Liu K; Watanabe E; Kokubo H
J Comput Aided Mol Des; 2017 Feb; 31(2):201-211. PubMed ID: 28074360
[TBL] [Abstract][Full Text] [Related]
10. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding.
Foloppe N; Chen IJ
Bioorg Med Chem; 2016 May; 24(10):2159-89. PubMed ID: 27061672
[TBL] [Abstract][Full Text] [Related]
11. Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations.
Uehara S; Tanaka S
J Chem Inf Model; 2017 Apr; 57(4):742-756. PubMed ID: 28388074
[TBL] [Abstract][Full Text] [Related]
12. Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening.
Arcon JP; Defelipe LA; Lopez ED; Burastero O; Modenutti CP; Barril X; Marti MA; Turjanski AG
J Chem Inf Model; 2019 Aug; 59(8):3572-3583. PubMed ID: 31373819
[TBL] [Abstract][Full Text] [Related]
13. Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design.
Hernández-Rodríguez M; Rosales-Hernández MC; Mendieta-Wejebe JE; Martínez-Archundia M; Basurto JC
Curr Med Chem; 2016; 23(34):3909-3924. PubMed ID: 27237821
[TBL] [Abstract][Full Text] [Related]
14. Molecular Dynamics as a Tool for Virtual Ligand Screening.
Menchon G; Maveyraud L; Czaplicki G
Methods Mol Biol; 2018; 1762():145-178. PubMed ID: 29594772
[TBL] [Abstract][Full Text] [Related]
15. Flexibility and explicit solvent in molecular-dynamics-based docking of protein-glycosaminoglycan systems.
Samsonov SA; Gehrcke JP; Pisabarro MT
J Chem Inf Model; 2014 Feb; 54(2):582-92. PubMed ID: 24479827
[TBL] [Abstract][Full Text] [Related]
16. Molecular dynamics simulations and novel drug discovery.
Liu X; Shi D; Zhou S; Liu H; Liu H; Yao X
Expert Opin Drug Discov; 2018 Jan; 13(1):23-37. PubMed ID: 29139324
[TBL] [Abstract][Full Text] [Related]
17. Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study.
Liu K; Kokubo H
J Chem Inf Model; 2017 Oct; 57(10):2514-2522. PubMed ID: 28902511
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. 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]
20. Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery.
Sabanés Zariquiey F; Jacoby E; Vos A; van Vlijmen HWT; Tresadern G; Harvey J
J Chem Inf Model; 2022 Feb; 62(3):533-543. PubMed ID: 35041430
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
