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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 servers

Description

URL

Refs.

Ligand-based drug design

 BioTriangle

Compute descriptors for compounds, protein, DNA and their interaction cross-terms

http://biotriangle.scbdd.com/

 [285]

 ChemDes

Computes 3679 molecular descriptors and 59 fingerprint types for compounds

http://www.scbdd.com/chemdes/

 [286]

 ChemBench

Enables QSAR model building via pre-defined workflow

http://chembench.mml.unc.edu/

 [287]

 OCHEM

Online platform providing storage for QSAR data and workflow for model building

http://www.ochem.eu/

 [288]

 PUMA

Performs analysis and visualization of chemical diversity

https://www.difacquim.com/d-tools/

 [289]

Structure-based drug design

 HADDOCK

Performs information-driven docking of biomolecular complexes (e.g. DNA, proteins, peptides, etc.)

http://haddock.science.uu.nl/services/HADDOCK2.2/

 [290]

 FlexServ

Performs coarse-grained determination of protein dynamics

http://mmb.pcb.ub.es/FlexServ/

 [291]

 MDWeb

Provides standard protocol for preparing structures, run standard molecular dynamics simulations and analyze trajectories

http://mmb.irbbarcelona.org/MDWeb/

 [292]

 PoseView

Displays simple molecular interaction diagram of protein-ligand complexes

http://www.zbh.uni-hamburg.de/poseview

 [293]

 SwissModel

Predicts protein structures via template-based homology

https://swissmodel.expasy.org/

 [294]