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From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study.
Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ. Warszycki D, et al. J Chem Inf Model. 2017 Feb 27;57(2):311-321. doi: 10.1021/acs.jcim.6b00263. Epub 2017 Jan 18. J Chem Inf Model. 2017. PMID: 28055203 Free PMC article.
In this paper we shed new light on the 3D pharmacological properties of the 5-HT(1A) receptor by using a ligand-guided approach (ALiBERO) grounded in the Internal Coordinate Mechanics (ICM) docking platform. Starting from a homology template and set of known actives, the m …
In this paper we shed new light on the 3D pharmacological properties of the 5-HT(1A) receptor by using a ligand-guided approach (ALiBERO …
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.
Rueda M, Totrov M, Abagyan R. Rueda M, et al. J Chem Inf Model. 2012 Oct 22;52(10):2705-14. doi: 10.1021/ci3001088. Epub 2012 Sep 17. J Chem Inf Model. 2012. PMID: 22947092 Free PMC article.
The LiBERO method relies on the use of ligand information for selecting the best performing individual pockets from ensembles derived from normal-mode analysis or Monte Carlo. Here we present ALiBERO, a new computational tool that has expanded the pocket selection from sin …
The LiBERO method relies on the use of ligand information for selecting the best performing individual pockets from ensembles derived from n …