Computer-aided drug design (CADD) softwares

Quantum Bio Solutions LLC	http://www.qbio.co.kr
Insilicotech Co., Ltd	http://www.insilicotech.co.kr
T&J Tech Inc.	http://www.tnjtech.co.kr
Advanced Chemistry Development, Inc. (ACD/Labs)	http://www.acdlabs.com/home
Chemical Computing Group (MOE)	http://www.chemcomp.com/index.htm
Molsoft LLC (ICM)	http://www.molsoft.com/index.html
MEDIT SA (Med-SuMo)	http://medit-pharma.com
OpenEye (OMEGA, ROCS, etc)	http://www.eyesopen.com
Inte:Ligand (LogandScout)	http://www.inteligand.com
Cambridge Crystallographic Data Centre (GOLD suite)	http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx
Schrödinger(Maestro, PyMOL)	http://www.schrodinger.com
Accelrys (Discovery Studio, Pipeline Pilot)	http://www.accelrys.com
Certara (Tripos SYBYL, 3D Explorer)	http://www.certara.com/products
Cresset(Flare)	https://www.cresset-group.com/software/flare

Biomolecular simulations

Molecular dynamics (MD) simulation & analysis

NAMD	http://www.ks.uiuc.edu/Research/namd
VMD	http://www.ks.uiuc.edu/Research/Vmd
GROMACS	http://www.gromacs.org
CHARMM	http://www.charmm.org

Quantum mechanics

Gaussian	http://gaussian.com

Molecular modeling tools & web-servers

Similarity search

BLAST	http://blast.ncbi.nlm.nih.gov/Blast.cgi

Multiple sequence alignment (MSA) & visualization

BLAST	http://blast.ncbi.nlm.nih.gov/Blast.cgi
Clustal Omega	http://www.ebi.ac.uk/Tools/msa/clustalo
ClustalW2	http://www.ebi.ac.uk/Tools/msa/clustalw2
Muscle	http://www.ebi.ac.uk/Tools/msa/muscle
T-Coffee	http://www.ebi.ac.uk/Tools/msa/tcoffee
MAFFT	http://www.ebi.ac.uk/Tools/msa/mafft
CD-HIT	http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi
Jalview	http://www.jalview.org
WebLogo	http://weblogo.Berkeley.edu

Secondary structure prediction

PSIPRED	http://bioinf.cs.ucl.ac.uk/psipred

Homology modeling, model validation & refinement

MODELLER	http://salilab.org/modeller
ModEval Model Evaluation Server	http://modbase.compbio.ucsf.edu/evaluation
Structural analysis and Verification Server	http://nihserver.mbi.ucla.edu/SAVES/

Protein structure alignment

SALIGN	http://modbase.compbio.ucsf.edu/salign
FAST	http://biowulf.bu.edu/FAST
MultiProt	http://bioinfo3d.cs.tau.ac.il/MultiProt
SuperPose	http://wishart.biology.ualberta.ca/SuperPose
Pairwise Dali	http://ekhidna.biocenter.helsinki.fi/dali_lite/start
Dali Server	http://ekhidna.biocenter.helsinki.fi/dali_server/start

Multiple receptor conformations (MRC)

Multiple Receptor Conformations Web server	http://abagyan.ucsd.edu/MRC

Ligand force field generation

SwissParam	http://swissparam.ch

Receptor-ligand interaction diagram

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

Drug discovery platform

Open PHACTS Discovery Platform	http://www.openphacts.org/explorer

Databases

Literature search

NCBI PubMed	http://www.ncbi.nlm.nih.gov/pubmed?itool=toolbar
SciFinder Web	https://scifinder.cas.org/scifinder
Web of Science	http://apps.webofknowledge.com
Journal Citation Reports(JCR)	http://admin-apps.webofknowledge.com/JCR/JCR?PointOfEntry=Home&SID=W2B7APQp1Ym6mF6CDRH

Proteins

RCSB Protein Data Bank (PDB)	http://www.pdb.org/pdb/home/home.do
Relibase : Search protein-ligand structures in PDB	http://relibase.ccdc.cam.ac.uk/account_utilities/login_form.php
Binding MOAD : Protein-ligand structures in PDB	http://www.bindingmoad.org
ExPASy : Bioinformatics Resource Portal	http://www.expasy.org
Structural Classification of Proteins (SCOP)	http://scop.mrc-lmb.cam.ac.uk/scop
Pfam Database	http://pfam.sanger.ac.uk
Superfamily	http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html
ModBase : comparative protein structure models	http://modbase.compbio.ucsf.edu
Orientations of Proteins in Membranes	http://opm.phar.umich.edu
GPCR Database	http://www.gpcr.org/7tm

Chemicals

ZINC Database	http://zinc.docking.org
PubChem Projects	http://pubchem.ncbi.nlm.nih.gov
BindingDb : The Binding Database	http://www.bindingdb.org/bind/index.jsp
Cambridge Crystallographic Data Center(CCDC)	http://www.ccdc.cam.ac.uk/pages/Home.aspx

Chemical vendors

Asinex	http://www.asinex.com/index.html
ChemBridge Corporation	http://www.chembridge.com/index.php
ChemDiv	http://chemdiv.com
Maybridge	http://www.maybridge.com
Life Chemicals	http://www.lifechemicals.com
Otava Ltd	http://www.otavachemicals.com/about/overview
Vitas-M Laboratory	http://www.vitasmlab.com
Ambinter	http://www.ambinter.com

Journals

Medicinal chemistry

Journal of Medicinal Chemistry	http://pubs.acs.org/journal/jmcmar
ACS Medicinal Chemistry Letters	http://pubs.acs.org/journal/amclct
European Journal of Medicinal Chemistry	http://www.journals.elsevier.com/european-journal-of-medicinal-chemistry
ChemMedChem	http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1860-7187
MedChemComm	http://pubs.rsc.org/en/journals/journalissues/md#!recentarticles&all
Bioorganic & Medicinal Chemistry	http://www.journals.Elsevier.com/bioorganic-and-medicinal-chemistry
Bioorganic & Medicinal Chemistry Letters	http://www.journals.Elsevier.com/bioorganic-and-medicinal-chemistry-letters

Molecular modeling

Journal of Chemical Information and Modeling	http://pubs.acs.org/journal/jcisd8
Journal of Computer-Aided Molecular Design	http://link.springer.com/journal/10822
Journal of Molecular Graphics and Modelling	http://www.journals.elsevier.com/journal-of-molecular-graphics-and-modelling
PLOS Computational Biology	http://www.ploscompbiol.org

Multidisciplinary - Chemistry

Angewandte Chemie International Edition	http://onlinelibrary.wiley.com/doi/10.1002/anie.v49:43/issuetoc
Journal of the American Chemical Society	http://pubs.acs.org/journal/jacsat
Nature Chemistry	http://www.nature.com/nchem/index.html
Nature Chemical Biology	http://www.nature.com/nchembio/index.html

Multidisciplinary

Proceedings of the National Academy of Sciences of the United States of America	http://www.pnas.org
PLOS One	http://www.plosone.org

Others

Nature Structural & Molecular Biology	http://www.nature.com/nsmb/index.html
The Journal of Biological Chemistry	http://www.jbc.org
Journal of Molecular Biology	http://www.journals.Elsevier.com/journal-of-molecular-biology

Ewha

Ewha Womans University	http://www.ewha.ac.kr
Ewha Womans University – Eureka Portal	http://eportal.ewha.ac.kr
Ewha Womans University – Cyber campus	http://cyber.ewha.ac.kr
Ewha Womans University - College of Pharmacy	http://home.ewha.ac.kr/~pharm21
Ewha Womans University – The Graduate School	http://graduate.ewha.ac.kr
Ewha Womans University - Library	http://lib.ewha.ac.kr
Ewha Womans University – Language center	http://elc.ewha.ac.kr/LangCenter/kor/index.jsp
Ewha Womans University – Health service center	http://euhs.ewha.ac.kr