Free Resources
Bioinformatics Resources Directory
117+ free and open-source bioinformatics tools and databases, organized by research area — genomics, proteomics, drug discovery, cancer, microbiology, and more. Built for scientists, students, and researchers who don't have a budget for paid platforms.
Prefer something built-in? Try the PradeepBio Tools hub💳 Paid / Registration-Heavy Tools
Useful tools that are not fully free — included for completeness, kept separate so the directory above stays 100% free-first.
MASCOT
PaidPeptide/protein identification from mass spec data — limited free searches, paid for full use.
UCSF ChimeraX
Free tierAdvanced molecular visualization — free for academic use, license required otherwise.
Mendeley
Free tierReference manager — free tier with storage limits.
HADDOCK
Free tierProtein–protein and protein–ligand docking — free tier queues, paid for priority access.
🔗 Also Explore — Recommended External Tools
These tools don't have a public API we can integrate natively, but are highly recommended and free to use directly.
HDOCK
↗Template-based and ab initio protein–protein and protein-DNA/RNA docking. Free academic use, results returned in ~10–20 min.
SAVES / ERRAT / PROCHECK
↗UCLA structure validation suite: ERRAT, Verify3D, PROCHECK, WHATCHECK — the standard tools for validating homology models before publication.
PDBsum
↗Graphical summary of any PDB entry — secondary structure, ligand interactions, Ramachandran and more, all on one page.
ProTox-3 — Toxicity Prediction
↗Predict oral toxicity, hepatotoxicity, and other endpoints for a compound from SMILES. Free, no registration required.
ABCpred — B-Cell Epitope Prediction
↗Predict linear B-cell epitopes in an antigen sequence using a recurrent neural network — useful for vaccine design workflows.
SwissTargetPrediction
↗2D+3D similarity-based target prediction for small molecules across human, mouse, and rat proteomes. No registration needed.
STS Bioinformatics — Gel Simulator
↗UIC's online gel electrophoresis simulator — useful as a reference alongside our built-in Gel Electrophoresis tool.
GenScript Online Tools
↗Suite of molecular biology tools including codon optimization, primer design, and protein analysis. Some features require a free account.
ADMETlab 3.0 (full platform)
↗The complete ADMETlab 3.0 web platform — 119 ADMET endpoints, batch mode, molecular editor, and decision-support features beyond our built-in ADMET tool.
Listed tools are maintained by their respective institutions and developers (NCBI, EMBL-EBI, Broad Institute, and others). PradeepBio does not host or modify any linked tool — this page is a curated index only. Always check each tool's own license and usage terms before use in published research. Spotted an outdated link or have a tool to suggest? Use the Feedback button in the site header.