# ProteinIQ > Browser-based bioinformatics tools for protein, DNA, RNA, ligand, and structure analysis. ProteinIQ helps researchers run computational biology analyses from a web workspace with documented inputs, tracked jobs, downloadable outputs, and shared team access. Public pages below are the best starting points for AI agents. For complete discovery, use the XML sitemaps listed here. **When to use ProteinIQ** Use ProteinIQ when an agent needs to run established bioinformatics methods for protein, DNA, RNA, ligand, or structure work without managing local scientific software or compute infrastructure. Best-fit jobs include choosing a documented tool, validating its accepted inputs and settings, running one analysis, composing a multi-step workflow, monitoring execution, and retrieving structured results or files. Use literature databases for paper discovery and use the original scientific publication when a method needs interpretation beyond the documented tool contract. **How agents should call ProteinIQ** For discovery, read this file, the linked tool documentation, and the XML sitemaps. For programmatic work, use the ProteinIQ REST API, Python SDK, or ProteinIQ MCP server with a workspace API key. Inspect the tool contract before submitting, preserve its scientific defaults and units, use an idempotency key for retryable writes, and retrieve every returned result and file. Browser pages remain available when a person needs to review inputs, costs, or outputs interactively. **Access notes** Public documentation, guides, blog posts, solution pages, pricing, security, and tool landing pages are intended for discovery. The OpenAPI contract and API documentation are public. User jobs, files, settings, billing management, admin pages, and authenticated API data are private application surfaces. For complete discovery, use the XML sitemaps below. Public pages also have a Markdown version: append `.md` to the page URL (for example `/docs.md`, or `/index.md` for the homepage), or send `Accept: text/markdown`. ## Core Navigation - [Home](https://proteiniq.io/): ProteinIQ overview and main product entry point. - [Tools](https://proteiniq.io/app/tools): Browse browser-based bioinformatics tools by category. - [ProteinIQ documentation](https://proteiniq.io/docs): Platform docs for jobs, files, credits, billing, and account setup. - [OpenAPI](https://proteiniq.io/openapi.json): Machine-readable OpenAPI 3.1 contract for the public API. - [Guides](https://proteiniq.io/guides): Educational guides for computational biology and bioinformatics topics. - [Blog](https://proteiniq.io/blog): Product updates and applied bioinformatics articles. - [Pricing](https://proteiniq.io/pricing): Plans, credits, billing, and commercial-use tiers. - [Security](https://proteiniq.io/security): Security and data handling overview. ## Developer Resources - [ProteinIQ REST API documentation](https://proteiniq.io/docs/api): API overview for tools, jobs, results, files, workflows, and projects. - [ProteinIQ OpenAPI contract](https://proteiniq.io/openapi.json): Machine-readable OpenAPI 3.1 contract for generating clients and validating requests. - [ProteinIQ API authentication](https://proteiniq.io/docs/api/authentication): Workspace API key format, bearer authentication, scopes, and security guidance. - [ProteinIQ MCP server](https://proteiniq.io/mcp): Remote MCP transport endpoint; connect using a ProteinIQ API key. - [ProteinIQ MCP setup](https://proteiniq.io/docs/api/mcp): When to use MCP, client configuration, available actions, and safe execution flow. - [ProteinIQ Python SDK](https://proteiniq.io/docs/api/python-sdk): Installation and reference for the maintained ProteinIQ Python client. ## Sitemaps - [Sitemap Index](https://proteiniq.io/sitemap-index.xml): Canonical XML sitemap index for search engines. - [Page Sitemap](https://proteiniq.io/sitemap-pages.xml): Core public pages and category hubs. - [Tool Sitemap](https://proteiniq.io/sitemap-tools.xml): All public tool pages. - [Guide Sitemap](https://proteiniq.io/sitemap-guides.xml): All public educational guide pages. - [Blog Sitemap](https://proteiniq.io/sitemap-blog.xml): All public blog posts. ## Documentation - [Welcome](https://proteiniq.io/docs): Find your starting point in the ProteinIQ documentation - [API](https://proteiniq.io/docs/api): Run ProteinIQ analyses, manage workspace files, and retrieve results from code - [Changelog](https://proteiniq.io/docs/changelog): Everything new on the ProteinIQ platform. - [Start guide](https://proteiniq.io/docs/start-guide): Run a Protein parameters analysis with an example sequence, inspect the output, and reopen your result - [Concepts](https://proteiniq.io/docs/concepts): Understand how workspaces, tools, jobs, results, files, and workflows fit together in ProteinIQ - [Quickstart](https://proteiniq.io/docs/api/quickstart): Quote, submit, monitor, and download an ESMfold job with a complete Python script - [Authentication](https://proteiniq.io/docs/api/authentication): Create, scope, test, and revoke workspace API keys - [Jobs](https://proteiniq.io/docs/jobs): Find analyses, understand job statuses, download results, and manage sharing - [Projects](https://proteiniq.io/docs/projects): Create projects, organize related analyses and files, and move or delete project resources - [Tools](https://proteiniq.io/docs/api/tools): Discover API tools and inspect accepted inputs, settings, outputs, and credit models - [Credits](https://proteiniq.io/docs/credits): Check workspace credit balances, allowances, expiration, and usage history - [Jobs](https://proteiniq.io/docs/api/jobs): Submit, quote, list, inspect, share, and cancel ProteinIQ API jobs - [Workflows](https://proteiniq.io/docs/workflows): Create connected analyses, run workflows, review outputs, and manage retries - [Batches](https://proteiniq.io/docs/batches): Run one tool across a dataset and review its jobs together - [Job credit usage](https://proteiniq.io/docs/job-billing): Understand fixed-price charges, time-based authorizations, spending limits, and job refunds - [Results](https://proteiniq.io/docs/api/results): Retrieve structured job results and download available output files - [Creating a batch](https://proteiniq.io/docs/batches/creating-a-batch): Choose a tool, prepare inputs, review jobs and submit a batch - [Files](https://proteiniq.io/docs/api/files): Upload, list, reference, and delete workspace files through the ProteinIQ API - [Workflow credit usage](https://proteiniq.io/docs/workflow-billing): Set workflow spending limits and understand estimates, pauses, and retry costs - [Workflows](https://proteiniq.io/docs/api/workflows): Validate, start, monitor, curate, cancel, and retry published ProteinIQ workflows through the API ## Tool Pages with Documentation - [AbLang Online](https://proteiniq.io/app/ablang): Run AbLang online to restore antibody residues, generate sequence or residue embeddings, and download amino-acid likelihood scores for heavy or light chains. - [AbLang-2 Online](https://proteiniq.io/app/ablang-2): AbLang-2 scores antibody sequences online, returning pseudo-likelihoods and 480-dimensional embeddings for paired or unpaired heavy-light chains, no setup. - [ABodyBuilder3 Online](https://proteiniq.io/app/abodybuilder3): ABodyBuilder3 predicts antibody heavy-light variable-domain structures online from VH and VL sequences, returning PDB files and confidence data. - [ADMET-AI Online](https://proteiniq.io/app/admet-ai): ADMET-AI predicts ADMET properties online, returning per-compound tables, DrugBank percentiles, structural alerts, radial plots, and files with no setup. - [Admetica Online](https://proteiniq.io/app/admetica): Admetica predicts 22 ADMET endpoints online, returning selected Caco-2, CYP, hERG, half-life, LD50, ids, SMILES, and result columns with no setup needed. - [AF-Cluster Online](https://proteiniq.io/app/af-cluster): AF-Cluster clusters protein MSAs online, returning cluster and control A3M files, assignments, metadata, PCA or t-SNE plots, and logs. - [AF2BIND Online](https://proteiniq.io/app/af2bind): Run AF2BIND online to predict protein ligand-binding residues with p(bind) scores, ranked residue tables, scored PDB files, and downloadable outputs. - [AF2Dock Online](https://proteiniq.io/app/af2dock): Run AF2Dock online for protein-protein docking from receptor and ligand structures, with ranked complex PDB files, iPTM scores, chain-restored PDB files, and confidence files. - [Aggrescan3D Online](https://proteiniq.io/app/aggrescan3d): Aggrescan3D scores protein aggregation online, returning residue scores, per-chain plots, summary JSON, and scored PDB files for review, no install needed. - [AIMNet2 Online](https://proteiniq.io/app/aimnet2): Run AIMNet2 online for molecular energy, force, charge, stress, and Hessian prediction from XYZ, SDF, PDB, or CIF coordinates. - [Aliphatic Index Calculator Online](https://proteiniq.io/app/aliphatic-index): Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability. - [AllMetal3D Online](https://proteiniq.io/app/allmetal3d): AllMetal3D predicts metal and water sites online, returning location, identity, geometry confidence, PDB coordinates, and CUBE files with no setup needed. - [AlphaFlow Online](https://proteiniq.io/app/alphaflow): AlphaFlow generates protein ensembles online, returning sample PDB structures, multi-model PDB files, data tables, and optional A3M files with no setup. - [AlphaFold Database Download](https://proteiniq.io/app/alphafold-database-download): Download AlphaFold DB predicted structures and confidence files by UniProt accession. - [AlphaFold2 Online](https://proteiniq.io/app/alphafold-2): AlphaFold2 predicts protein structures online, returning ranked PDB models, pLDDT, PAE, pTM, ipTM, MSA outputs, and multimer files with no install needed. - [AlphaGenome Online](https://proteiniq.io/app/alphagenome): AlphaGenome predicts RNA-seq variant effects online, returning run details, track metadata, and reference-alternate arrays in downloadable NPZ files. - [Amino Acid Composition Calculator](https://proteiniq.io/app/amino-acid-composition): Free online tool to analyze amino acid composition of protein sequences. Calculate the percentage and frequency of each amino acid in proteins. Supports FASTA format and batch a... - [ANARCI Online](https://proteiniq.io/app/anarci): ANARCI numbers antibody and TCR sequences online, returning chain type, species, V/J germline calls, scores, native numbering files, and domain spans, no setup. - [ANARCII Online Server](https://proteiniq.io/app/anarcii): ANARCII numbers antibody, TCR, and VNAR/VHH sequences online and renumbers structures, returning source CSV, MessagePack, scores, spans, and residue calls. - [AntiFold Online](https://proteiniq.io/app/antifold): AntiFold designs antibody sequences online, returning sampled CDR or framework mutations, likelihood scores, sequence tables, and FASTA files with no setup. - [AutoDock Vina Online](https://proteiniq.io/app/autodock-vina): AutoDock Vina docks ligands online, returning 3D poses, affinity scores in kcal/mol, pose tables, and downloadable structure files with no install needed. - [AutoDock-GPU Online](https://proteiniq.io/app/autodock-gpu): AutoDock-GPU docks ligands online, returning ranked poses, AutoDock4 binding energies in kcal/mol, PDBQT files, data tables, and viewer output, no setup. - [BindCraft Online](https://proteiniq.io/app/bindcraft): BindCraft designs protein binders online, returning accepted sequences, PDB designs, pLDDT, pTM, i pTM, i pAE, RMSD, filters, and files, no setup needed. - [BioEmu Online](https://proteiniq.io/app/bioemu): Sample protein monomer equilibrium ensembles with BioEmu. Select a checkpoint and sampling controls, supply an A3M alignment, and download native result files. - [BioPhi Online](https://proteiniq.io/app/biophi): BioPhi humanizes antibodies online, returning Sapiens sequences, OASis humanness scores, native result files, and downloadable tables with no setup needed. - [BLAST Protein Search Online](https://proteiniq.io/app/blast-search): Search Swiss-Prot or PDB protein sequences with BLAST+, native alignments, E-values, bit scores, coverage and downloadable results. - [Boltz ADME online](https://proteiniq.io/app/boltz-adme): Predict LogD, permeability and solubility for up to 1,000 SMILES with Boltz ADME. Download the results as CSV. - [Boltz Protein Screen online](https://proteiniq.io/app/boltz-protein-screen): Screen up to 500 binder sequences against a protein target. Get ranked binders, scores and predicted complexes. - [Boltz Sequence Redesign online](https://proteiniq.io/app/boltz-sequence-redesign): Redesign chosen residues of a protein structure with Boltz Sequence Redesign. Get FASTA sequences, scores and predicted complexes. - [Boltz Small Molecule Explore online](https://proteiniq.io/app/boltz-small-molecule-explore): Explore a large CSV or TSV SMILES library against a protein target, scoring only a set budget of molecules. - [Boltz Small Molecule Screen online](https://proteiniq.io/app/boltz-small-molecule-screen): Screen up to 1,000 SMILES against a protein target. Get ranked molecules, scores and predicted complexes. - [Boltz-2 Server](https://proteiniq.io/app/boltz-2): Use the ProteinIQ Boltz-2 online webserver to predicts molecular complexes, returning ranked structures, confidence, affinity probability, IC50 estimates, and CIF or PDB files w... - [Boltz-2.1 online](https://proteiniq.io/app/boltz-2-1): Predict protein, nucleic acid and ligand complex structures with Boltz-2.1. Get CIF files, confidence metrics and binding metrics. - [BoltzGen Online](https://proteiniq.io/app/boltzgen): Run BoltzGen online to generate ranked binder sequences, complex and binder-only CIF structures, native metrics, refolding checks, and result reports. - [BoltzMol-1 online](https://proteiniq.io/app/boltzmol-1): Design purchasable small molecules for a protein target with BoltzMol-1. Get ranked SMILES, scores and predicted complexes. - [BoltzProt-1 online](https://proteiniq.io/app/boltzprot-1): Design mini-protein, peptide, nanobody or antibody binders for a protein target with BoltzProt-1. - [Brenk filter Online](https://proteiniq.io/app/brenk-filter): Brenk filter screens compounds online, returning alert counts, matched SMARTS patterns, pass or fail results, SMILES rows, and exports with no setup needed. - [Butina clustering Online](https://proteiniq.io/app/butina-clustering): Group molecules by fingerprint distance using RDKit Butina clustering. - [Calculate Instability Index Online](https://proteiniq.io/app/instability-index): Calculate the protein instability index online from FASTA sequences. Compare dipeptide-based scores and stability predictions at the threshold of 40. - [Calculate isoelectric point (pI) online](https://proteiniq.io/app/pi-calculator): Free online tool to calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge. ## Guides - [How many chromosomes do different species have?](https://proteiniq.io/guides/chromosome-counts-by-species): Dogs have 78 chromosomes, cats 38, humans 46 and chimpanzees 48. See which other animals share our 46, which have the most and fewest, and why counts differ. - [How long is human DNA?](https://proteiniq.io/guides/how-long-is-dna): Each human cell holds about 2 m of DNA, and the whole body about 14 billion km, or 96 times the distance from Earth to the Sun. Each base pair adds 0.34 nm. - [How many amino acids are there?](https://proteiniq.io/guides/how-many-amino-acids-are-there): Proteins use 20 standard amino acids. Selenocysteine and pyrrolysine bring the genetically encoded set across life to 22, nine are essential in the human diet, and about 500 occ... - [How many ATP are produced in fermentation?](https://proteiniq.io/guides/how-many-atp-are-produced-in-fermentation): Lactic acid and alcoholic fermentation each yield two net ATP per glucose. All of that ATP comes from glycolysis; the fermentation reactions add no more. - [How many genes do humans have?](https://proteiniq.io/guides/how-many-genes-do-humans-have): Humans have about 20,000 protein-coding genes: 19,442 in GENCODE v50, 19,878 in Ensembl 116 and 19,838 in CHESS 3.1.3. With RNA genes and pseudogenes, GENCODE lists 78,733. - [How much DNA do humans share with other animals?](https://proteiniq.io/guides/human-animal-dna-similarity): Pigs do not share 98% of human DNA. Measured the same way for every species, a typical pig protein is 89% identical to the human one, against 99% for chimpanzees and 86% for rats. - [How much DNA do humans share with bananas?](https://proteiniq.io/guides/human-banana-dna-similarity): Yes, but not 50%. About 18% of human genes have a banana counterpart, their proteins are about 40% identical, and only 0.08% of the human genome matches. - [How big is the human genome?](https://proteiniq.io/guides/human-genome-size): The human genome is about 3.1 billion base pairs long per chromosome set, or 6.3 billion per cell. Compare GRCh38, T2T-CHM13 and genome file sizes in GB. - [What are the largest and smallest cells in the human body?](https://proteiniq.io/guides/largest-and-smallest-cells): The egg is the largest human cell at about 115 µm, sperm the smallest and a sensory neuron the longest. We also ranked 401 human cell types by mass. - [What is the largest protein?](https://proteiniq.io/guides/largest-protein): PKZILLA-1 is the largest known protein at 45,212 amino acids. Titin is the largest human protein, and von Willebrand factor the largest in blood plasma. - [How many proteins are there?](https://proteiniq.io/guides/number-of-proteins): Humans have about 20,000 proteins, one per protein-coding gene. UniProt lists 150 million protein records across all life. See what each count measures. - [What is the smallest protein?](https://proteiniq.io/guides/smallest-protein): The smallest natural protein is an 11-amino-acid fruit fly peptide. In humans, MOTS-c has 16 and RPL41 has 25. The smallest unit of a protein is an amino acid. - [AlphaFold license and commercial use](https://proteiniq.io/guides/alphafold-license-commercial-use): AlphaFold 2 and the AlphaFold Database allow commercial use, while the AlphaFold 3 weights and AlphaFold Server do not. See what each license allows and which models, including... - [DockQ score explained](https://proteiniq.io/guides/dockq): DockQ scores how closely a predicted protein complex matches a reference interface, from 0 to 1, with CAPRI cutoffs at 0.23, 0.49 and 0.80. Learn how it combines fnat, iRMSD and... - [What the MolProbity score and clashscore mean](https://proteiniq.io/guides/molprobity-score): The MolProbity score combines clashscore, rotamer outliers and Ramachandran favored residues into one number on the scale of crystallographic resolution. Learn what counts as go... - [What is PAE, and how to read a PAE plot](https://proteiniq.io/guides/pae): PAE (predicted aligned error) is the pairwise confidence matrix that AlphaFold, Boltz and Chai-1 write next to a predicted structure. Learn how to read its blocks and stripes an... - [How to read a Ramachandran plot](https://proteiniq.io/guides/ramachandran-plot): A Ramachandran plot shows the phi and psi backbone angles of every residue in a protein. Learn what the regions mean, what percentages a good structure has, and how to tell a mo... - [What is RMSD, and what counts as a good value](https://proteiniq.io/guides/rmsd): RMSD is the average distance between matched atoms of two structures, in ångströms. Learn the formula, when to superimpose, and what values count as good for proteins, docked po... - [How to tell if a predicted protein structure is reliable](https://proteiniq.io/guides/structure-prediction-confidence): A predicted structure is reliable for a question when the scores that answer that question agree. Read pLDDT, PAE, pTM and ipTM in order, rescore interfaces with ipSAE, then che... - [What is a Vina score, and what counts as good](https://proteiniq.io/guides/vina-score): The AutoDock Vina score is a docking score in kcal/mol, not a measured binding energy. Learn what the output columns mean, why there is no universal good score, and how far Vina... ## Blog - [Design and screen molecules with Boltz models](https://proteiniq.io/blog/boltz-models): Eight new tools bring Boltz-2.1, BoltzMol-1, BoltzProt-1 and the Boltz screening, redesign and ADME models to ProteinIQ, with credit pricing, workflows and batch runs. - [Introducing the API and Python SDK](https://proteiniq.io/blog/api-and-python-sdk): A public API and a Python SDK are now available, giving scripts, notebooks, and services the same tools, jobs, files, and results that power the web app. - [Cheaper pricing for individual users](https://proteiniq.io/blog/cheaper-pricing): ProteinIQ now has a lower-cost paid plan, simpler academic and commercial tiers, and clearer licensing boundaries. - [Build bioinformatics pipelines with workflows](https://proteiniq.io/blog/workflows): Build reusable bioinformatics pipelines by connecting ProteinIQ tools, adding filters and breakpoints, and running the whole analysis from one canvas.