Grand Challenge 3
I've written a couple of docking/virtual screening workflows using SMINA, a freely available tool DOI. There are a number of other alternatives and it is very difficult to get good comparisons which is why the Grand Challenges are useful.
The Grand Challenge 3 (GC3) is a blinded prediction challenge for the computational chemistry community, with components addressing pose-prediction, affinity ranking, and free energy calculations. GC3 is based on six different protein targets, Cathepsin S and five different kinases, and is separated into five subchallenges, some of which involve multiple protein targets. Only Cathepsin S is associated with cocrystal structures, so the kinase components of this challenge focus on affinity ranking and/or free energy predictions. Three of the datasets, Cathepsin S, JAK2 and TIE2, include a free energy prediction component.
This is an ideal opportunity to test novel algorithms on a carefully curated dataset.
Computational practices often employ a number of computational algorithms and dataset preparation steps for meaningful results. D3R will provide a forum for deposition, dissemination and discussion of such workflows through this website. Workflows will represent methods used successfully in the blinded challenges and methods donated by our pharmaceutical and/or academic collaborators. GitHub.
In Stage 1 September 1 - October 1, your predicted poses for the 24 ligands, in a coordinate system aligned with the S04-bound Cathepsin S structure provided in the inputs. Your predicted affinities, or affinity rankings, for all 136 compounds and/or your predicted absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds. When Stage 1 closes, we will release the crystallographic poses of the 24 ligands.
In Stage 2 October 1 - December 1, your predictions of the affinity rankings of all 136 compounds and/or absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds.