# What will you discover with ProteinIQ?

From docking to design to dynamics, explore how researchers run reproducible bioinformatics workflows without writing code.

[Start a workflow](https://proteiniq.io/app/workflows/templates)[Browse tools](https://proteiniq.io/app/tools)

Showing 60 of 60 use cases

[Molecular docking ## AI molecular docking Use AI docking models to generate protein–ligand poses, compare their confidence, and check whether the predicted structures are chemically plausible. Explore](https://proteiniq.io/use-cases/ai-molecular-docking)[Molecular dynamics simulation ## All-atom molecular dynamics Run atomistic protein simulations with explicit force-field, solvent, ensemble, and trajectory settings. Explore](https://proteiniq.io/use-cases/all-atom-molecular-dynamics)[Protein design ## Antibody design Generate and redesign antibodies or nanobodies with antigen, framework, CDR, structure, and developability context. Explore](https://proteiniq.io/use-cases/antibody-design)[Protein structure prediction ## Antibody structure prediction Predict antibody variable-domain structures from paired chains and examine framework, CDR-loop, and residue-level confidence. Explore](https://proteiniq.io/use-cases/antibody-structure-prediction)[Molecular docking ## Antibody–antigen docking Explore antibody–antigen binding orientations using structural models and available epitope or paratope evidence. Explore](https://proteiniq.io/use-cases/antibody-antigen-docking)[Phylogenetic analysis ## Bayesian phylogenetics Prepare a reviewed protein alignment, plan priors and independent MCMC runs, and create an IQ-TREE cross-check before external Bayesian inference. Explore](https://proteiniq.io/use-cases/bayesian-phylogenetics)[Molecular docking ## Blind docking Search broadly across a prepared protein when the ligand-binding site is unknown or poorly characterized. Explore](https://proteiniq.io/use-cases/blind-docking)[Molecular dynamics simulation ## Coarse-grained molecular dynamics Review compatible coarse-grained trajectories without treating bead-level dynamics as atomistic detail. Explore](https://proteiniq.io/use-cases/coarse-grained-molecular-dynamics)[Molecular docking ## Consensus docking Compare results across docking engines while preserving each method’s native poses, scores, and confidence values. Explore](https://proteiniq.io/use-cases/consensus-docking)[Protein design ## De novo protein design Generate proteins beyond known templates, then connect backbone generation, sequence assignment, refolding, and candidate review. Explore](https://proteiniq.io/use-cases/de-novo-protein-design)[Sequence alignment ## DNA sequence alignment Align nucleotide sequences while preserving strand, ambiguity, coordinate, and coding-frame context. Explore](https://proteiniq.io/use-cases/dna-sequence-alignment)[Molecular dynamics simulation ## Enhanced sampling molecular dynamics Run metadynamics or simulated tempering in OpenMM. Use the separate review workflow for existing trajectories, with reweighting and convergence assessed externally. Explore](https://proteiniq.io/use-cases/enhanced-sampling-molecular-dynamics)[Molecular docking ## Ensemble docking Dock a ligand across multiple prepared receptor conformations and retain state-specific poses for comparison. Explore](https://proteiniq.io/use-cases/ensemble-docking)[Protein design ## Enzyme design Build protein scaffolds around catalytic geometry, redesign ligand-aware sequences, and connect computation to biochemical testing. Explore](https://proteiniq.io/use-cases/enzyme-design)[Molecular docking ## Flexible molecular docking Model ligand binding poses while accounting for selected side-chain flexibility or learned receptor movement. Explore](https://proteiniq.io/use-cases/flexible-molecular-docking)[Sequence alignment ## Global sequence alignment Compare complete sequences end to end and make terminal gaps, full-length coverage, and score definitions explicit. Explore](https://proteiniq.io/use-cases/global-sequence-alignment)[Virtual screening ## High-throughput virtual screening Prepare and partition a large compound library, apply staged filters, run reproducible batches, and aggregate ranked results without losing failures or method settings. Explore](https://proteiniq.io/use-cases/high-throughput-virtual-screening)[Protein structure prediction ## Homology modeling Build protein models from related experimental templates, then examine alignment assumptions, geometry, and structural agreement. Explore](https://proteiniq.io/use-cases/homology-modeling)[Protein design ## Inverse folding Design amino-acid sequences for a fixed protein backbone, compare complementary models, and refold candidates before selection. Explore](https://proteiniq.io/use-cases/inverse-folding)[Virtual screening ## Inverse virtual screening Evaluate one compound across a curated target panel, retain target-specific poses and scores, and review target or off-target hypotheses. Explore](https://proteiniq.io/use-cases/inverse-virtual-screening)[Virtual screening ## Ligand-based virtual screening Compare a compound library with known active ligands using molecular descriptors, fingerprints, pharmacophores, or learned features, then review and export a traceable shortlist. Explore](https://proteiniq.io/use-cases/ligand-based-virtual-screening)[Sequence alignment ## Local sequence alignment Score the best-matching subsequences without forcing unrelated flanks into an end-to-end comparison. Explore](https://proteiniq.io/use-cases/local-sequence-alignment)[Phylogenetic analysis ## Maximum likelihood phylogenetics Align homologous protein sequences, infer independent IQ-TREE and RAxML-NG trees, and compare models, topology, and branch support. Explore](https://proteiniq.io/use-cases/maximum-likelihood-phylogenetics)[Molecular docking ## Molecular docking Compare docking methods by molecular partners, binding-site evidence, flexibility, and receptor-state coverage. Explore](https://proteiniq.io/use-cases/molecular-docking)[Molecular dynamics simulation ## Molecular dynamics simulation Choose a molecular-dynamics method by resolution, sampling problem, perturbation, and intended observable. Explore](https://proteiniq.io/use-cases/molecular-dynamics-simulation)[Protein structure alignment ## Multiple protein structure alignment Compare three or more protein structures in one shared correspondence, then review conserved cores, outliers, and alignment consistency. Explore](https://proteiniq.io/use-cases/multiple-protein-structure-alignment)[Sequence alignment ## Multiple sequence alignment Align homologous sequence sets with multiple methods, review conserved columns and gaps, and keep method uncertainty visible. Explore](https://proteiniq.io/use-cases/multiple-sequence-alignment)[Sequence alignment ## Pairwise sequence alignment Compare two sequences directly, preserve the aligned strings and scoring settings, and separate correspondence from similarity scores. Explore](https://proteiniq.io/use-cases/pairwise-sequence-alignment)[Protein design ## Peptide design Generate compact peptide candidates for a target or property objective, then screen activity and developability signals. Explore](https://proteiniq.io/use-cases/peptide-design)[Protein structure prediction ## Peptide structure prediction Predict plausible peptide conformations while preserving cyclization, sequence length, flexibility, and model-specific structural assumptions. Explore](https://proteiniq.io/use-cases/peptide-structure-prediction)[Molecular docking ## Peptide–protein docking Model flexible peptide binding poses against prepared protein receptors and compare alternative interaction hypotheses. Explore](https://proteiniq.io/use-cases/peptide-protein-docking)[Virtual screening ## Pharmacophore-based virtual screening Define a three-dimensional interaction-feature model, prepare candidate conformers, rank feature matches, and review a chemically diverse shortlist. Explore](https://proteiniq.io/use-cases/pharmacophore-based-virtual-screening)[Phylogenetic analysis ## Phylogenetic analysis Infer and compare protein trees with inspectable alignments, models, branch support, native reports, and explicit uncertainty. Explore](https://proteiniq.io/use-cases/phylogenetic-analysis)[Protein design ## Protein binder design Design compact proteins against a specified target surface, then connect sequence optimization, refolding, and interface review. Explore](https://proteiniq.io/use-cases/protein-binder-design)[Protein structure prediction ## Protein complex structure prediction Predict multi-chain protein assemblies and compare interface geometry, stoichiometry assumptions, confidence, and model agreement. Explore](https://proteiniq.io/use-cases/protein-complex-structure-prediction)[Protein design ## Protein design Compare protein-design tasks by what is being created, the evidence supplied, the model output, and the experiments needed next. Explore](https://proteiniq.io/use-cases/protein-design)[Protein structure alignment ## Protein fold recognition Identify a plausible structural fold for a difficult protein sequence, then review candidate models and templates without hiding the external threading step. Explore](https://proteiniq.io/use-cases/protein-fold-recognition)[Molecular dynamics simulation ## Protein molecular dynamics simulation Prepare a protein, run conventional GROMACS molecular dynamics, and retain trajectories, energies, settings, and structural analyses. Explore](https://proteiniq.io/use-cases/protein-molecular-dynamics-simulation)[Protein structure prediction ## Protein secondary structure prediction Predict residue-level helices, strands, and coils from sequence, then compare them with coordinate-derived assignments. Explore](https://proteiniq.io/use-cases/protein-secondary-structure-prediction)[Sequence alignment ## Protein sequence alignment Align amino-acid sequences with protein-aware methods and interpret conservation in structural and functional context. Explore](https://proteiniq.io/use-cases/protein-sequence-alignment)[Protein design ## Protein sequence design Generate or optimize amino-acid sequences against structural, functional, stability, and developability objectives. Explore](https://proteiniq.io/use-cases/protein-sequence-design)[Protein structure alignment ## Protein structure alignment Choose pairwise comparison, database search, fold-recognition review, or multiple-structure review according to the evidence and output you need. Explore](https://proteiniq.io/use-cases/protein-structure-alignment)[Protein structure prediction ## Protein structure prediction Compare prediction methods by starting evidence, molecular system, output, confidence, and downstream research workflow. Explore](https://proteiniq.io/use-cases/protein-structure-prediction)[Protein structure alignment ## Protein structure search Search large protein-structure databases with a query fold, then inspect ranked neighbors, coverage, scores, and alignments. Explore](https://proteiniq.io/use-cases/protein-structure-search)[Molecular docking ## Protein–ligand docking Generate and compare plausible small-molecule binding poses within a prepared protein target and defined search region. Explore](https://proteiniq.io/use-cases/protein-ligand-docking)[Molecular docking ## Protein–protein docking Model how two prepared protein structures may assemble and interact within a biologically plausible complex. Explore](https://proteiniq.io/use-cases/protein-protein-docking)[Molecular dynamics simulation ## Replica exchange molecular dynamics Review reconstructed replica trajectories while keeping exchange statistics and equilibrium claims anchored to the external ensemble. Explore](https://proteiniq.io/use-cases/replica-exchange-molecular-dynamics)[RNA structure prediction ## RNA 3D structure prediction Generate and compare atomic RNA structure hypotheses with multiple biomolecular foundation models. Explore](https://proteiniq.io/use-cases/rna-3d-structure-prediction)[RNA structure prediction ## RNA secondary structure prediction Predict RNA base pairing, minimum-free-energy structures, alternative folds, and local accessibility from sequence. Explore](https://proteiniq.io/use-cases/rna-secondary-structure-prediction)[RNA structure prediction ## RNA structure prediction Choose the RNA prediction workflow that matches the biological question: intramolecular base pairing, atomic 3D coordinates, or intermolecular RNA binding. Explore](https://proteiniq.io/use-cases/rna-structure-prediction)[RNA structure prediction ## RNA–RNA interaction prediction Compare joint folding, duplex hybridization, accessibility-aware binding, and fast query–target screening for two RNAs. Explore](https://proteiniq.io/use-cases/rna-rna-interaction-prediction)[Sequence alignment ## Sequence alignment Choose the alignment scope that matches your evidence, then run a connected workflow with explicit inputs, settings, and outputs. Explore](https://proteiniq.io/use-cases/sequence-alignment)[Virtual screening ## Shape-based virtual screening Prepare reference ligands and candidate conformers, compare three-dimensional shape and chemical features, then review a diverse shortlist in one connected workflow. Explore](https://proteiniq.io/use-cases/shape-based-virtual-screening)[Protein structure prediction ## Single-sequence protein structure prediction Predict three-dimensional protein structures directly from one sequence without supplying alignments, templates, or homologous sequences. Explore](https://proteiniq.io/use-cases/single-sequence-protein-structure-prediction)[Molecular dynamics simulation ## Steered molecular dynamics Review structures and compatible trajectories from steered simulations while keeping force, work, pathway, and protocol claims tied to the external run. Explore](https://proteiniq.io/use-cases/steered-molecular-dynamics)[Sequence alignment ## Structure-based sequence alignment Use three-dimensional geometry to derive residue correspondence when sequence similarity alone is too weak or ambiguous. Explore](https://proteiniq.io/use-cases/structure-based-sequence-alignment)[Virtual screening ## Structure-based virtual screening Prepare a target structure, review a compound library, generate ranked poses with GNINA, and inspect pose-quality and ADMET results in one editable workflow. Explore](https://proteiniq.io/use-cases/structure-based-virtual-screening)[Protein structure prediction ## Transmembrane protein structure prediction Predict membrane-protein folds and examine hydrophobic segments, topology context, confidence, and explicit membrane-orientation limitations. Explore](https://proteiniq.io/use-cases/transmembrane-protein-structure-prediction)[Virtual screening ## Virtual screening Compare in silico screening approaches, then start an online workflow for compound preparation, ranking, review, and export. Explore](https://proteiniq.io/use-cases/virtual-screening)[Sequence alignment ## Whole genome alignment Compare genome assemblies with coordinate-aware alignment, dot plots, variant tables, and retained delta files. Explore](https://proteiniq.io/use-cases/whole-genome-alignment)