Database

• NCBI Protein
• UniProt

PDB Database

• RCSB PDB
• Protein Data Bank in Europe
• AlphaFold Protein Structure Database

PDB viewer

• RasMol
• PyMOL
  • PyMOL Wiki
  • PyMOL Command Refs
  • PyMOL Script Repository (Queen's U BioChem)

PDB comparison

• TM-align
• TM-score

PDB similarity

• CATH

PDB Docking

• HDOCK

• AlphaFold2
• RoseTTAFold

• SCOP2
• CATH

• GROMOS
• NAMD
• AMBER
• CHARMM

Database

• Pfam
• NCBI Conserved Domain Database
• PROSITE
• InterPro
• SMART

Motif Search

• Motif
• HMMER
• MEME
• Motif Scan
• NCBI CDD
• PROSITE
• MEROPS
• PWMTools

Signal peptides for subcellular localization

• SignalP
• DeepLoc
• TargetP
• MULocDeep
• DeepSig
• YLoc
• LocTree3
• SubCons
• PSORTdb
• NLSdb

Programs

• BPP
• Branchpointer
• SVM-BPfinder
• HSF
• LaBranchoR
• RNABPS

Programs

• RNAfold
• Mfold/UNAfold
• CONTRAfold
• ContextFold
• TORNADO
• SimFold
• SPOT-RNA
• MXfold2

Database

• NCBI
• EMBL-EBI
• ENCODE
• BioCyc
• GTEx
• Gene Ontology

Database

• ENCODE ChIP-Seq
• JASPAR
• TRANSFAC Public
• TRANSFAC

Programs

• MATCH
• gene-regulation.com

Database

• miRBase
• DIANA TOOLS
• miRCancer
• miRGator
• miRSel
• PolymiRTS
• TransmiR
• SomamiR DB

Programs

• miRDB
• TargetScan
• DIANA TOOLS
• MIRSYSTEM

• Expasy
• Broad Institute
• EMBL-EBI Services
• NCBI Resources
• DDBJ Services

• STRING
• KEGG
• DAVID
• reactome
• METACYC
• Pathway Commons

• MAGeCK
• PBNPA
• BAGEL2
• STARS
• CERES
• STARS