FM@H
  • Find protein targets for existing antimalarial compounds.
    • This can be used for further drug discovery.
    • Compounds that are shown to inhibit these targets can be developed into antimalarial drugs.

  • Find novel inhibitors for proteins of interest.
    • Each target protein will be searched by all available compounds.
    • Researchers interested in specific proteins will find potential inhibitors in our results lists.
    • Once validated, these could provide the basis for novel drug discovery.

Search data

If selecting 'best' or 'top 20' ligands, choose compound sets to include in the search:

*Note that if you choose a specific ligand with a specific receptor, the "sorting" option doesn't matter.
  • MMV400 = MalariaBox structural diversity, filtered, subset offered by MMV. [400]
  • MMV19k = All the hit compounds found by GSK, Novartis and the St. Jude's Children's Hospital. Curated by MMV. [18,924]
  • ChEMBL_Bioassays = All additional hit compounds (IC50 < 2 microMolar, whole organism growth assays) that are not represented in the MMV19k set. [4,262]
  • NPC = NCGC Pharmaceutical Collection of approved and investigational drugs. [2,549]
  • LiverStage = Novartis-GNF Malaria Liver Stage dataset P. yoelii schizont IC50 < 10 microMolar. [273]
  • XrayLig = X-ray co-crystal structure ligand molecules. (excluding solvent, salts, etc)
  • UCT = University of Cape Town lead compounds. [2]

Find Ligands


Please insert ligand name, ligand title or PubChemCID in the search box

The Plasmodium falciparum 3D7 genome contains 5,363 possible proteins. We used models created by the Sali lab (using MODELLER) for most of this work. [Orti, L., 2009].

  • SaliSite = All models that have structural identity to PDB structures with known ligands. [28]
  • SaliGood = All MODPIPE models with MPQS > 1,0. [1,426]
  • XrayAll = All P. fal. proteins that contain at least one X-ray structure. [140]
  • XrayLig = P. fal. X-ray structures containing a small molecule inhibitor. [49]

Find Protein receptor for docking


Please insert protein name or UniProtKB Code in the search box
  • Ligand preparation : MOE
  • Receptor preparation : MOE
  • Docking : Autodock Vina
  • Pocket detection : Fpocket
  • Distributed computation : BOINC
  • Database : MySQL
  • Analysis : Python, R
Zscore_rec
Zscore_lig
Zscore_sum
TDR score
FiND score
Binding Affinity
All the data (ranked by Zscore_sum)
All ligands for each receptor, ranked by BA (MMV data only)
All ligands for each receptor, ranked by BA
All ligands for each receptor, ranked by FiNDscore (MMV data only)
All ligands for each receptor, ranked by FiNDscore
All receptors for each ligand, ranked by BA (MMV data only)
All receptors for each ligand, ranked by BA
All receptors for each ligand, ranked by FiND score (MMV data only)
All receptors for each ligand, ranked by FiND score
Top 1 ligand for each receptor, ranked by BA (MMV data only)
Top 1 ligand for each receptor, ranked by BA
Top 1 ligand for each receptor, ranked by FiNDscore (MMV data only)
Top 1 ligand for each receptor, ranked by FiNDscore
Top 1 receptor for each ligand, ranked by BA (MMV data only)
Top 1 receptor for each ligand, ranked by BA
Top 1 receptor for each ligand, ranked by FiND score (MMV data only)
Top 1 receptor for each ligand, ranked by FiND score
Top 20 ligands for each receptor, ranked by BA (MMV data only)
Top 20 ligands for each receptor, ranked by BA
Top 20 ligands for each receptor, ranked by FiNDscore (MMV data only)
Top 20 ligands for each receptor, ranked by FiNDscore
Top 20 receptors for each ligand, ranked by BA (MMV data only)
Top 20 receptors for each ligand, ranked by BA
Top 20 receptors for each ligand, ranked by FiND score (MMV data only)
Top 20 receptors for each ligand, ranked by FiND score
List of the top 1000 rec-lig pairs ranked by Binding Affinity
List of the top 1000 rec-lig pairs ranked by FiND score
List of the top 1000 rec-lig pairs ranked by Zscore_lig
List of the top 1000 rec-lig pairs ranked by Zscore_rec
List of the top 1000 rec-lig pairs ranked by Zscore_sum
Binding Affinity scores in lig * rec matrix (data)
Binding Affinity scores in lig * rec matrix (errors)
FiND scores in lig * rec matrix
Ligand based Zscore (Zscore_lig) in lig * rec matrix
Receptor based Zscore (Zscore_rec) in lig * rec matrix
Zscore_sum data in lig * rec matrix
All FiND scores components
Means and StdDev for ligand based Zscore (Zscore_lig)
Means and StdDev for receptor based Zscore (Zscore_rec)
Ligand Efficiency
Ligand Efficiency scores in lig * rec matrix (data)
Ligand Efficiency scores in lig * rec matrix (errors)
Miscellaneous
All ligands in final results output
All receptors in final results output
Parser log file



Input data files

  • Ligands
    • pdb, pdbqt, mdb, sdf format
    • Includes: MMV400 [400], MMV19k (GSK, Novartis and the St. Jude's Children's Hospital) [18,924], ChEMBL_Bioassays [4,262], NPC [2,549], LiverStage [273], Xraylig [41], UCT [2].
  • Receptors
    • pdb, pdbqt, moe format
    • Includes: Saligood [4262], SaliSite [28], XrayAll [140].

Parsed data

  • Final CreateMatrix files (all subsets)
  • CreateMatrix (MMV only)

Scripts

  • Both python and bash scripts []