FightAIDS@home Phase 2

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FAH2 Experiments

Below is a comprehensive list of the experiment batches that have been (or are planned to be) launched on IBM's World Community Grid under FightAIDS@Home Phase II. The description for each group of batches contains a brief statement regarding the role of the experiments as well as receptor/ligand information, detailed batch list, and estimates for the number and completion status of workunits in the group.

Note regarding estimates: The estimates provided for the number of workunits (WUs) assume that all workunits run to completion without error. Thus the number of WUs actually completed will be higher due to the various complications that can arise in a computational grid. The completion estimate is also approximate and represents some combination of 1.) the percentage of BOINC results have been returned to the research team and 2.) the percentage of results that have been successfully post-processed and analyzed. As analysis of results is not fully automated, the completion estimates listed below may lag behind the percentage of results that have been returned to the research team. As of December 2016, the completion estimates should update roughly weekly.


Experiments 000819-001318

Experiments 819-1318 are the first set of simulations to refine FightAIDS@Home Phase 1 experiments in which compounds from the ZINC library were screened against HIV integrase.

Note that due to the upcoming release of asynchronous replica exchange, these simulations may be cut short and rerun with the new protocols.

Receptor Structure: HIV Integrase, PDB 3NF8, LEDFG binding site site
Detailed Experiment List: Available
Estimated WUs: 2,700,000
Complete: 0%

Experiments 000368-000818

Experiments 368-818 are a continuation of experiments 159-367 including a much expanded set of ligands.

Receptor Structure: HIV Integrase, PDB 3NF8, LEDFG binding site site
Detailed Experiment List: Available
Estimated WUs: 2,430,000
Complete: 80%

Experiments 000159-000367

Experiments 159-367 are composed of simulating a set of 209 ligands which are known to not bind well to the HIV Integrase LEDGF pocket. Performing these experiments will let us calibrate the results from previous and future simulations where ligands are strong binders.

Receptor Structure: HIV Integrase, PDB 3NF8, LEDFG binding site site
Detailed Experiment List: Available
Estimated WUs: 3,344,000
Complete: 100%

Experiments 000106-000158

Experiments 106-158 are composed of simulating the set of 53 protein-ligand complexes from experiments 0-105, except the starting conformations are those found in the crystal structures, not from docking. This provides us a baseline or best case scenario to evaluate how well BEDAM performs.

Receptor Structure: HIV Integrase, PDB 3NF8, LEDFG binding site site
Detailed Experiment List: Available
Estimated WUs: 424,000
Complete: 100%

Experiments 000000-000105

Experiments 0-105 are composed of simulating a set of 53 ligand-receptor complexes in two different ways. Batches that end with `-ls' are simulated with what we call `lambda scheduling', and batches without `-ls' are using independent sampling. This set of ligands is a known set of binders with known bound crystal structures (see here).

Receptor Structure: HIV Integrase, PDB 3NF8, LEDFG binding site site
Detailed Experiment List: Available
Estimated WUs: 13,780,000
Complete: 100%

FightAIDS@Home Phase 1 Experiments

For a complete description of the experimental status of Phase 1 results, consult the Phase 1 Status page here.