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Table 4 List of selected web applications for handling various bioinformatic and cheminformatic tasks belonging to either ligand-based or structure-based drug design approach

From: Towards reproducible computational drug discovery

Web serversDescriptionURLRefs.
Ligand-based drug design
 BioTriangleCompute descriptors for compounds, protein, DNA and their interaction cross-terms [285]
 ChemDesComputes 3679 molecular descriptors and 59 fingerprint types for compounds [286]
 ChemBenchEnables QSAR model building via pre-defined workflow [287]
 OCHEMOnline platform providing storage for QSAR data and workflow for model building [288]
 PUMAPerforms analysis and visualization of chemical diversity [289]
Structure-based drug design
 HADDOCKPerforms information-driven docking of biomolecular complexes (e.g. DNA, proteins, peptides, etc.) [290]
 FlexServPerforms coarse-grained determination of protein dynamics [291]
 MDWebProvides standard protocol for preparing structures, run standard molecular dynamics simulations and analyze trajectories [292]
 PoseViewDisplays simple molecular interaction diagram of protein-ligand complexes [293]
 SwissModelPredicts protein structures via template-based homology [294]