These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
6. Molecular recognition of RNA: challenges for modelling interactions and plasticity. Fulle S; Gohlke H J Mol Recognit; 2010; 23(2):220-31. PubMed ID: 19941322 [TBL] [Abstract][Full Text] [Related]
7. 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]
8. Accommodating protein flexibility for structure-based drug design. Lin JH Curr Top Med Chem; 2011; 11(2):171-8. PubMed ID: 20939792 [TBL] [Abstract][Full Text] [Related]
9. Using metadynamics and path collective variables to study ligand binding and induced conformational transitions. Bešker N; Gervasio FL Methods Mol Biol; 2012; 819():501-13. PubMed ID: 22183554 [TBL] [Abstract][Full Text] [Related]
10. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2. Athanasiou C; Vasilakaki S; Dellis D; Cournia Z J Comput Aided Mol Des; 2018 Jan; 32(1):21-44. PubMed ID: 29119352 [TBL] [Abstract][Full Text] [Related]
11. 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]
12. Towards accurate free energy calculations in ligand protein-binding studies. Steinbrecher T; Labahn A Curr Med Chem; 2010; 17(8):767-85. PubMed ID: 20088755 [TBL] [Abstract][Full Text] [Related]
13. The role of water molecules in computational drug design. de Beer SB; Vermeulen NP; Oostenbrink C Curr Top Med Chem; 2010; 10(1):55-66. PubMed ID: 19929830 [TBL] [Abstract][Full Text] [Related]
14. Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites. Broomhead NK; Soliman ME Cell Biochem Biophys; 2017 Mar; 75(1):15-23. PubMed ID: 27796788 [TBL] [Abstract][Full Text] [Related]
15. Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Moraca F; Amato J; Ortuso F; Artese A; Pagano B; Novellino E; Alcaro S; Parrinello M; Limongelli V Proc Natl Acad Sci U S A; 2017 Mar; 114(11):E2136-E2145. PubMed ID: 28232513 [TBL] [Abstract][Full Text] [Related]
16. A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein-protein and protein-ligand binding potencies. Wang J; Ishchenko A; Zhang W; Razavi A; Langley D Sci Rep; 2022 Feb; 12(1):2024. PubMed ID: 35132139 [TBL] [Abstract][Full Text] [Related]
17. Linear interaction energy: method and applications in drug design. Gutiérrez-de-Terán H; Aqvist J Methods Mol Biol; 2012; 819():305-23. PubMed ID: 22183545 [TBL] [Abstract][Full Text] [Related]
18. Electrostatics in proteins and protein-ligand complexes. Kukić P; Nielsen JE Future Med Chem; 2010 Apr; 2(4):647-66. PubMed ID: 21426012 [TBL] [Abstract][Full Text] [Related]
19. Free Energy Calculations for Protein-Ligand Binding Prediction. Jespers W; Åqvist J; Gutiérrez-de-Terán H Methods Mol Biol; 2021; 2266():203-226. PubMed ID: 33759129 [TBL] [Abstract][Full Text] [Related]
20. Predicting protein ligand binding motions with the conformation explorer. Flores SC; Gerstein MB BMC Bioinformatics; 2011 Oct; 12():417. PubMed ID: 22032721 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]