Misc. Servers - patrickchirdon/AIdrugdiscovery GitHub Wiki

Deepbind- can be used to score promoter sequences for

over 900 transcription factors. Computes a binding score

http://tools.genes.toronto.edu/deepbind/

https://github.com/jisraeli/DeepBind

Eukaryotic promoter db: https://epd.vital-it.ch/index.php

Pepcomposer- create peptides that have a high affinity for a

specific binding site

https://cassandra.med.uniroma1.it/pepcomposer/

webserver/pepcomposer.php

Foldx- score peptide peptide interactions http://foldxsuite.crg.eu/products#foldx_suite

Pafnucy-ligand docking https://gitlab.com/cheminfIBB/pafnucy

cell penetrating peptide- http://www.thegleelab.org/MLCPPExample.html

convert peptide to smiles- http://bioware.ucd.ie/~cyclops/cgi-bin/webpep.cgi

Stable/long half life peptides- http://crdd.osdd.net/cgibin/hlp/pep_both.pl

protein toxicity- prediction-http://crdd.osdd.net/raghava/toxinpred/design.php

smiles toxicity screen- http://xundrug.cn/moltox

bayes screen- given some common feature, ie toxic or not, c10 like or not etc, perform a ligand based screen, https://github.com/davidhoksza/bayescreen

can train bayes screen on tox21 data sets to recognize toxic compounds.

Tox21- Bioinf.jku.at/research/DeepTox/tox21.html

netphos- determine phosphorylation sites. http://www.cbs.dtu.dk/services/NetPhos/

Anti-viral compound prediction-- http://crdd.osdd.net/servers/avcpred/

anti-microbial peptide prediction-- http://cabgrid.res.in:8080/amppred/

protein binding site prediction- prediction of peptide binding sites on protein surfaces-- http://pepsite2.russelllab.org/

14-3-3 protein binding-- predict which phosphorylation sites YWHAE,YWHAB,YWHAW etc might bind, http://www.compbio.dundee.ac.uk/1433pred/

phosphorylation site prediction-- https://www.phosphosite.org/

lipidation site prediction-- http://lipid.biocuckoo.org

pharmacophore screen-- find top 300 proteins a given protein binds http://lilab.ecust.edu.cn/pharmmapper/help.php