text: 380,152,1231863479293874177,57640264,Ariane Nunes Alves,".@Rebecca_Wade_C , @DariaKokh and I wrote a review of computational methods to study ligand-protein binding kinetics. We assessed the performance of methods considering two benchmark systems, T4 lysozyme (T4L) and N-HSP90. (1/3) @HITStudies #compchem <LINK> <LINK> @Rebecca_Wade_C @DariaKokh @HITStudies The figure below shows the times required for different methods to simulate complexes with different exp. residence times (RT). In the last two years many methods to compute relative RT were published. An increase of four orders of magnitude in exp. RT leads to a smaller, (2/3) <LINK> @Rebecca_Wade_C @DariaKokh @HITStudies one order of magnitude increase in comp. time. For T4L, results indicate that good RT estimation can be achieved without exhaustive path sampling so long as the most probable paths are sampled (table below). Another highlight: two works aiming at computing RT prospectively. (3/3) <LINK> @_Maicol_ @Rebecca_Wade_C @DariaKokh @HITStudies thanks! 😊 @sowmyaindrakum1 @Rebecca_Wade_C @DariaKokh @HITStudies what i showed you in your visit is related, but not the same thing. @Jmondal_tifrh @Rebecca_Wade_C @DariaKokh @HITStudies thanks! 😊 @Herr_Flow @Rebecca_Wade_C @DariaKokh @HITStudies you are welcome! 😀 is the arXiv paper published? send me the link, so I can correct the citation later. our work is under review on COSB right now.",https://arxiv.org/abs/2002.08983,"Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling molecular dynamics simulation-based methods has been developed for computing drug-target binding kinetics and studying binding and unbinding mechanisms. Here, we assess the performance of these methods considering two benchmark systems in detail: mutant T4 lysozyme-ligand complexes and a large set of N-HSP90-inhibitor complexes. The results indicate that some of the simulation methods can already be usefully applied in drug discovery or lead optimization programs but that further studies on more high-quality experimental benchmark datasets are necessary to improve and validate computational methods. ","Recent progress in molecular simulation methods for drug binding