Curated Molecular Biology & Bioinformatics Directory
Bioinformatics & Molecular Biology Tools
Explore standard web platforms from DeepMind, NCBI, ExPASy, EMBL-EBI, and Broad Institute alongside CodonTable native instant converters.
Instant In-Browser Execution
CodonTable Native Translation Suite
Free client-side converters, interactive codon charts, and genetic calculators with zero server queue:
Free Native
Popular
DNA to Protein Converter
Convert DNA sequences to protein sequences with support for multiple genetic codes and reading frames
Free Native
DNA to RNA Converter
Transcribe DNA sequences to complementary RNA sequences with FASTA format support
Free Native
RNA to Protein Converter
Translate RNA sequences to protein sequences with support for multiple genetic codes and reading frames
Free Native
Popular
Codon to Anticodon Converter
Convert mRNA codons to complementary tRNA anticodons with 5' to 3' and 3' to 5' antiparallel pairing
Free Native
Popular
Sequence Translator
Comprehensive sequence translation tool supporting DNA and RNA to protein conversion
Free Native
Popular
Codon Table
Interactive codon table showing the genetic code with amino acid assignments
Free Native
Popular
Codon Wheel
Visual codon wheel representation of the genetic code for easy lookup
Free Native
Codon Hub
Comprehensive genetic code tools hub with interactive features
Free Native
Popular
GC Content Calculator
Calculate GC content percentage in DNA sequences
Next-Generation Foundation Models
AI & Biomolecular Foundation Models
Universal multi-entity complex prediction, variant effect modeling, and de novo protein generative models:
Industry Leading
FreeAlphaFold 3 Web Server
by Google DeepMind & Isomorphic Labs
Google DeepMind and Isomorphic Labs' flagship biomolecular modeling server, accurately predicting structures of proteins, DNA, RNA, ligands, ions, and chemical modifications in atomic detail.
#Protein-Nucleic Acid Complexes#AlphaFold 3#Ligand Docking
Featured AI
Research APIAlphaGenome
by Google DeepMind
DeepMind's unified genomic foundation model predicting the quantitative regulatory consequences of non-coding genetic variants on RNA-seq gene expression and chromatin epigenetics.
#Genomics#Deep Learning#Non-coding Variants
Popular
FreeAlphaFold Protein Structure Database
by Google DeepMind / EMBL-EBI
EMBL-EBI and Google DeepMind's public repository offering over 200 million AI-predicted 3D macromolecular structures across the tree of life with residue-level pLDDT confidence scores.
#Protein Folding#3D Coordinates#UniProt Coverage
Open Source
Open SourceBoltz-1
by Valence Labs / MIT
Valence Labs and MIT's state-of-the-art open-source biomolecular foundation model predicting complexes of proteins, RNA, DNA, and covalent chemical ligands under open MIT license.
#Open Source#AlphaFold3 Alternative#Biomolecular Complex
Fastest 3D
Open SourceESMFold
by Meta AI
Meta AI's ultra-fast atomic-resolution protein structure prediction engine powered by the 15-billion parameter ESM-2 language model, folding sequences in seconds without MSA searches.
#Protein Language Model#ESM-2#Single Sequence Folding
Revolutionary
Open SourceRFdiffusion
by University of Washington / Baker Lab
Baker Lab's generative diffusion foundation model for de novo protein design, functional motif scaffolding, binder design against target antigens, and symmetric oligomeric assemblies.
#Generative AI#De Novo Design#Diffusion Model
AI Model
FreemiumChai-1
by Chai Discovery
Multi-modal foundation model by Chai Discovery predicting binding affinities, protein-drug complexes, and multi-chain assemblies at near-experimental crystallization resolution.
#Drug Discovery#Protein-Ligand#Affinity Prediction
Top Research AI
FreemiumSciSpace (Typeset)
by SciSpace (Typeset.io)
Premier AI research copilot for biosciences and medicine: instant literature review, deep PDF chat with mathematical formulas, citation searching, and smart data extraction from papers.
#AI Research Copilot#Literature Review#Paper PDF Chat
Citation Standard
FreemiumScite.ai Smart Citations
by Scite LLC
Award-winning AI scientific platform evaluating over 1.2 billion citation statements to discover whether research findings are supported, mentioned, or contrasted by subsequent studies.
#Smart Citations#Evidence Checking#Literature Verification
Journal Ready
FreemiumPaperpal Academic AI
by Editage / Cactus Communications
Specialized generative AI academic writing and language editing tool trained on millions of published biomedical and science manuscripts to guarantee journal-ready submissions.
#Manuscript Polish#Academic Writing#Grammar & Clarity
Academic Standards · Alignment & Primers
Online Sequence Analysis & Alignment
NCBI BLAST, Primer-BLAST specificity checks, multiple sequence alignment, and UCSC In-Silico PCR:
Essential
Free WebNCBI BLAST
by NCBI / NIH
The gold-standard Basic Local Alignment Search Tool. Finds regions of local sequence similarity across nucleotide and protein databases with BLASTn, BLASTp, BLASTx, and tBLASTn.
Essential
Free WebNCBI Primer-BLAST
by NCBI / NIH
Automated PCR primer design server integrating Primer3 with whole-genome BLAST specificity checks to avoid non-specific amplification across transcriptomes and genomes.
Standard
Free WebClustal Omega
by EMBL-EBI
High-performance multiple sequence alignment (MSA) server by EMBL-EBI utilizing mBed guide trees and profile-profile Hidden Markov Model (HMM) algorithms.
Academic
Free WebMUSCLE
by Robert C. Edgar / EMBL-EBI
Renowned multiple sequence alignment tool achieving superior benchmark accuracy and rapid execution for large nucleotide and protein datasets.
Academic
Free WebT-Coffee
by Centre for Genomic Regulation (CRG) / EBI
Consistency-based multiple sequence alignment package combining pairwise global and local alignments, structural templates, and high-accuracy progressive algorithms.
Academic
Free WebUCSC In-Silico PCR
by UCSC Genome Browser Group
Instant genome-wide electronic PCR simulator mapping primer pairs against reference genomes (Human, Mouse, Rat, etc.) to detect amplicon sizes, introns, and genomic loci.
Academic
Free WebNCBI ORFfinder
by NCBI / NIH
Interactive open reading frame finder identifying all candidate protein-coding segments in DNA sequences using standard or non-standard genetic codes.
Native In-House
Free WebCodonTable Sequence Translator
by CodonTable (In-House)
Instant client-side 6-frame translation tool translating nucleotide sequences to protein sequences across forward and reverse-complement frames with open reading frame visualization.
Protein Biochemistry & 3D Structure
Protein Properties, Homology Modeling & 3D Viewers
Isoelectric point (pI), molecular weight calculation, automated homology modeling, and WebGL structure viewers:
Essential
FreeExPASy ProtParam (Compute pI/Mw)
by SIB Swiss Institute of Bioinformatics
The global standard for computing physical and chemical parameters of a protein: theoretical isoelectric point (pI), molecular weight, extinction coefficient, and instability index.
Standard
FreeSWISS-MODEL Homology Modeling
by Biozentrum Basel / SIB
Fully automated protein structure homology modeling server developed by the SIB. Connects raw sequence targets with experimental templates in the PDB.
Web 3D
Open SourceMol* (Molstar) 3D Viewer
by Mol* Consortium / RCSB PDB
Next-generation WebGL macromolecular 3D structure visualization library powering RCSB PDB and AlphaFold DB. Super-fast in-browser rendering of massive Cryo-EM and crystal structures.
Structure
FreeSignalP 6.0
by Technical University of Denmark (DTU)
Deep learning server predicting the presence, location, and cleavage site of five types of signal peptides across Archaea, Bacteria, and Eukarya.
Structure
FreeDeepTMHMM / TMHMM
by DTU Health Tech
Deep learning neural network predicting transmembrane helices, signal peptides, and topology of integral alpha-helical and beta-barrel membrane proteins.
Publication Standard
FreemiumiTOL (Interactive Tree Of Life)
by EMBL
Online tool for the display, manipulation, annotation, and publication-ready rendering of complex phylogenetic and evolutionary trees.
International Data Archives
Biological Databases & Genomic Repositories
Primary repositories for sequence annotations, structural biology, and functional pathways:
Authority
FreeUniProt Knowledgebase
The world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional annotation data (Swiss-Prot & TrEMBL).
Authority
FreeRCSB Protein Data Bank (PDB)
Single global repository of experimental 3D structures of biological macromolecules determined by X-ray crystallography, Cryo-EM, and NMR spectroscopy.
Database
FreeNCBI GenBank
NIH genetic sequence database, an annotated collection of all publicly available DNA and RNA sequences across the tree of life (part of INSDC).
Database
FreeEnsembl Genome Browser
Comprehensive genome browser dedicated to vertebrate gene models, comparative genomics, variant annotations (VEP), and transcriptional regulation.
Popular
FreeSTRING Database
Known and predicted protein-protein interactions (PPI) covering direct physical bindings and indirect functional associations across millions of proteins.
Database
FreemiumKEGG Pathway
Kyoto Encyclopedia of Genes and Genomes: curated pathway maps representing molecular interaction, reaction, and relation networks for metabolism, diseases, and drugs.
Database
FreeEnrichr
Ma'ayan Lab's comprehensive gene set enrichment analysis web server with hundreds of curated gene set libraries across pathways, disease, and transcription factors.
Database
FreeUCSC Genome Browser
The interactive online genome browser providing real-time visualization of annotations, ENCODE epigenetic tracks, evolutionary conservation scores (PhyloP), and genetic variations.
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