Skip to main content

Advertisement

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-termshttp://biotriangle.scbdd.com/ [285]
 ChemDesComputes 3679 molecular descriptors and 59 fingerprint types for compoundshttp://www.scbdd.com/chemdes/ [286]
 ChemBenchEnables QSAR model building via pre-defined workflowhttp://chembench.mml.unc.edu/ [287]
 OCHEMOnline platform providing storage for QSAR data and workflow for model buildinghttp://www.ochem.eu/ [288]
 PUMAPerforms analysis and visualization of chemical diversityhttps://www.difacquim.com/d-tools/ [289]
Structure-based drug design
 HADDOCKPerforms information-driven docking of biomolecular complexes (e.g. DNA, proteins, peptides, etc.)http://haddock.science.uu.nl/services/HADDOCK2.2/ [290]
 FlexServPerforms coarse-grained determination of protein dynamicshttp://mmb.pcb.ub.es/FlexServ/ [291]
 MDWebProvides standard protocol for preparing structures, run standard molecular dynamics simulations and analyze trajectorieshttp://mmb.irbbarcelona.org/MDWeb/ [292]
 PoseViewDisplays simple molecular interaction diagram of protein-ligand complexeshttp://www.zbh.uni-hamburg.de/poseview [293]
 SwissModelPredicts protein structures via template-based homologyhttps://swissmodel.expasy.org/ [294]