The list of Life Science Servers

We include those publicly available biology-related web servers here, that are in working condition, and the instructions are written in English. If you wish us to include your server here, please send your request to, with a one-line description. Standard listing is offered  free of charge, and we list your server until it is available.

Gene databases

GenBank  NIH genetic sequence database      The EMBL Nucleotide Sequence Database                 
GeneCards  summary & links for each gene     Database of Single Nucleotide Polymorphisms
Unigene : An organized view of the transcriptome DDBJ: DNA Data Bank of Japan
Cystic Fibrosis Mutation Database          RefSeq genomic DNA and transcripts database
ENTREZ Gene Genes and mapped phenotypes
Saccharomyces Genome Database (SGD)
Fourmidable database for ant genomics
Candida Genome Database (CGD)
WORMBASE: the genome of C. elegans
ZEBRAFISH mutation resource
GOBASE: The Organelle Genome Database
MGC: Mammalian Gene Collection

Gene sequence search and alignment servers

BLAST - Pasteur Institute
BLAST - EMBL BiSearch BiSearch is a primer-design algorithm for DNA sequences
BLAST - NIAS DNA Bank BLAST - ExPasy (Switzerland)
FASTA - GeneStream IGH Montpellier FASTA - DDBJ (Japan)
FASTA - DISC/AFFRC EMBOSS Matcher: Waterman-Eggert algorithm alignment
KEGG GENES Genes in high-quality genomes PARALIGN: sequence similarity search
FramePlot - Protein Coding Region Prediction in Bacterial DNA  ORF Finder - Open Reading Frame Finder at - NCBI (US)
Translate - Translates a nucleotide sequence to a protein sequence Transeq - Nucleotide to protein translation
Align Pairwise global and local alignment tool WSEmboss CpG Plot/CpGreport   CpG Island finder and plotting tool WSEmboss
Pepstats/Pepwindow/Pepinfo EMBOSS programs for basic protein sequence analysis WSEmboss OMA browser: orthology prediction server
Genewise DNA search accomodating introns and frame-shifting NeedleN sequence alignment
smiRNAdb - Mammalian small RNAs (Reverse)-Transcription and Translation Tool
IMGT - ImMunoGeneTics db EPD - Eukaryotic Promoter db
KEGG GENOME Genomes in organisms Secondary Structure Alignment tool
EMBOSS Supermatcher for local pair-wise alignments

Protein sequence servers

UniProtKB Protein sequence database    
Chordata protein annotation program
KEGG GENES Genes and proteins MSA Multiple Sequence Alignment
SwissAlign Protein sequence alignment with Smith-Waterman algorithm
ScanSite: Search biological databases for regular expressions
Radar - Repeat detection in protein sequences REPRO - Repeat detection in protein sequences
HMMER: sequence analysis with hidden Markov models DAS predicts transmembrane segments by "Dense Alignment Surface" method
Anchor identifies protein segments that reside in disordered regions TRUST - Repeat detection in protein sequences
HeliQuest - helix prediction server XSTREAM - Repeat detection and architecture modeling in protein sequences
PATTINPROT Pattern search server Hits - Protein sequence to motifs server
ProFound - Search known protein sequences with peptide mass information PRINTS: Protein fingerprint server
ProteinProspector - Tools for peptide mass data Mascot - Peptide mass fingerprinting
SMART - Simple Modular Architecture Research Tool ELM -  resource for finding functional sites in proteins
HAMAP: High-quality Automated and Manual Annotation of microbial Proteomes PPSEARCH - Scans a sequence against PROSITE
InterPro - Integrated Resources of Proteins Domains and Functional Sites ViralZone - Portal to viral UniProtKB/Swiss-Prot entries
PRINTS - Protein Motif fingerprint db Gene3D - Structural and Functional Annotation of Protein Families
CYSREDOX Cysredox predicts the redox state of cysteins in proteins PIRSF - Protein classification system
PSORT-B  for prediction of localization in Gram-negative bacterial proteins DAS-TMfilter predicts transmembrane segments by "Dense Alignment Surface" method
PFAM protein family annotations
BOXSHADE: Pretty printing of multiple alignment files

Protein 3D structure servers

RCSB Protein Data Bank    
Worldwide Protein Data Bank
PDBsum is  an at-a-glance overview of PDB structures DECOMP is a PDB protein-ligand decomposition server
WikiPDB is a social site for improving and annotating PDB, external API's allowed PDBWiki is a PDB annotation tool
iPfam: protein domain interactions database PDBj Protein Data Bank Japan
CCDC Cambridge Crystallographic Data Center
HCA Hydrophobic cluster database
GENO3D: Automatic modeling of 3d protein structures
FoldAlign: RNA fold predictor
SWISS-MODEL - An automated protein modelling server TopPred - Topology prediction of membrane proteins
HMMTOP - Prediction of transmembrane helices and topology of proteins TMpred - Prediction of transmembrane regions and protein orientation
PDBTM is a transmembrane protein selection tool from the PDB. TOPDOM a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins
SOSUI - Prediction of transmembrane regions TMHMM - Prediction of transmembrane helices in proteins
Paircoil - Prediction of coiled regions in proteins Paircoil2 - Prediction of the parallel coiled regions of proteins
Multicoil - Prediction of multi-stranded coiles STRAP - A structural alignment program for proteins
AGADIR - to predict the helical content of peptides TopMatch-web - Structure comparison of proteins
TLSMD - Protein flexibility prediction GlobPlot - Protein disorder/order/globularity/domain predictor
DisEMBL - Protein disorder prediction MeDor - Metaserver or Disorder
POODLE - Prediction Of Order and Disorder by machine LEarning DAS - Prediction of transmembrane regions
TatP - Twin-arginine signal peptides TargetP - Prediction of subcellular location
IUPred Prediction of Intrinsically Unstructured Proteins SCIDE identifies the stabilization center residues in known protein structures
SCPRED predicts stabilization center residues in proteins with unknown structure SRide identifies the stabilizing residues in proteins
TMDET: the detection of the transmembrane regions of membrane proteins by using their 3D structure only TOPDB a collection of transmembrane protein datasets containing experimentally derived topology informat

Protein interaction network servers

DIP - Database of Interacting Proteins NASCENT PPI network generation tool         
HPRD - Human Protein Reference Database IntAct Interacting proteins database
BioGRID - General Repository for Interaction Dataset PPI - Jena Protein-Protein Interaction db
BOND - Biomolecular Object Network Databank MINT - Molecular INTeraction database  
NetworkBLAST finds complexes in PPI networks that are conserved in evolution IsoRank: Global PPI network alignemnt tool
TrypanoPPI: Trypanosome target prediction based on PPI network analisys MIPS Mammalian Protein-Protein Interaction Database
Homomint is a human entry point to MINT APID Agile Protein Interaction Data Analyzer
DP-Bind sequence-based prediction of DNA-binding residues in DNA-binding proteins. SNAPPI structures and interfaces for protein interactions
ICBS A database of PPIs mediated by interchain �-sheet formation
HIV PI Database Interactions between HIV and host proteins at the NCBI MIPS CYGD Saccharomyces cerevisiae genome database
iPfam: protein domain interactions database

Metabolic networks and metabolomics servers

UniPathway - Metabolic pathways database   
KEGG PATHWAY Pathway maps for systemic functions
KEGG RCLASS Reaction class KEGG RPAIR Reactant pair chemical transformations
KEGG ENZYME Enzyme nomenclature KEGG PATHWAY Pathway maps
KEGG COMPOUND Metabolites and other small molecules Human Meatabolome Database (HMDB)
Golm metabolome database
Metabolome Express: a forum for metabolomics data
Serum Metabolome Database of the human serum
Tumor metabolome server
ExPASy biochemical pathways is the digitized version of the Roche wallchart
ChemMine metabolomic compound mining db
MetaCyC metabolic pathways
ChEBI compound database
Plant Metabolic Network (PMN) pathways

Nanobiotechnology servers

BROWNIAN: 3D Brownian motion simulator

Metagenomics and phylogeny servers

Biology WorkBench: an integrated tool for sequence alignment and phylogeny
MG-RAST: metagenomics analysis server
Web MGA: webserver for metagenomics analysis
AmphoraNet: Phylogenetic annotation of metagenomic sequences
Real Time Metagenomics annotation

Other directories of LifeSci servers

List of Protein Disorder Predictors KEGG: Kyoto Encyclopedia of Genes and Genomes
ExPASy Tools
ENTREZ cross-database search
BioSpider: a bio search engine
The  Peptide Resource Page

Last modified: November 14, 2013