What will you discover with ProteinIQ?

Molecular docking

Use AI docking models to generate protein–ligand poses, compare their confidence, and check whether the predicted structures are chemically plausible.

Molecular dynamics simulation

Run atomistic protein simulations with explicit force-field, solvent, ensemble, and trajectory settings.

Protein design

Generate and redesign antibodies or nanobodies with antigen, framework, CDR, structure, and developability context.

Protein structure prediction

Predict antibody variable-domain structures from paired chains and examine framework, CDR-loop, and residue-level confidence.

Molecular docking

Explore antibody–antigen binding orientations using structural models and available epitope or paratope evidence.

Phylogenetic analysis

Prepare a reviewed protein alignment, plan priors and independent MCMC runs, and create an IQ-TREE cross-check before external Bayesian inference.

Molecular docking

Search broadly across a prepared protein when the ligand-binding site is unknown or poorly characterized.

Molecular dynamics simulation

Review compatible coarse-grained trajectories without treating bead-level dynamics as atomistic detail.

Molecular docking

Compare results across docking engines while preserving each method’s native poses, scores, and confidence values.

Protein design

Generate proteins beyond known templates, then connect backbone generation, sequence assignment, refolding, and candidate review.

Sequence alignment

Align nucleotide sequences while preserving strand, ambiguity, coordinate, and coding-frame context.

Molecular dynamics simulation

Run metadynamics or simulated tempering in OpenMM. Use the separate review workflow for existing trajectories, with reweighting and convergence assessed externally.

Molecular docking

Dock a ligand across multiple prepared receptor conformations and retain state-specific poses for comparison.

Protein design

Build protein scaffolds around catalytic geometry, redesign ligand-aware sequences, and connect computation to biochemical testing.

Molecular docking

Model ligand binding poses while accounting for selected side-chain flexibility or learned receptor movement.

Sequence alignment

Compare complete sequences end to end and make terminal gaps, full-length coverage, and score definitions explicit.

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.

Protein structure prediction

Build protein models from related experimental templates, then examine alignment assumptions, geometry, and structural agreement.

Protein design

Design amino-acid sequences for a fixed protein backbone, compare complementary models, and refold candidates before selection.

Virtual screening

Evaluate one compound across a curated target panel, retain target-specific poses and scores, and review target or off-target hypotheses.

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.

Sequence alignment

Score the best-matching subsequences without forcing unrelated flanks into an end-to-end comparison.

Phylogenetic analysis

Align homologous protein sequences, infer independent IQ-TREE and RAxML-NG trees, and compare models, topology, and branch support.

Molecular docking

Compare docking methods by molecular partners, binding-site evidence, flexibility, and receptor-state coverage.

Molecular dynamics simulation

Choose a molecular-dynamics method by resolution, sampling problem, perturbation, and intended observable.

Protein structure alignment

Compare three or more protein structures in one shared correspondence, then review conserved cores, outliers, and alignment consistency.

Sequence alignment

Align homologous sequence sets with multiple methods, review conserved columns and gaps, and keep method uncertainty visible.

Sequence alignment

Compare two sequences directly, preserve the aligned strings and scoring settings, and separate correspondence from similarity scores.

Protein design

Generate compact peptide candidates for a target or property objective, then screen activity and developability signals.

Protein structure prediction

Predict plausible peptide conformations while preserving cyclization, sequence length, flexibility, and model-specific structural assumptions.

Molecular docking

Model flexible peptide binding poses against prepared protein receptors and compare alternative interaction hypotheses.

Virtual screening

Define a three-dimensional interaction-feature model, prepare candidate conformers, rank feature matches, and review a chemically diverse shortlist.

Phylogenetic analysis

Infer and compare protein trees with inspectable alignments, models, branch support, native reports, and explicit uncertainty.

Protein design

Design compact proteins against a specified target surface, then connect sequence optimization, refolding, and interface review.

Protein structure prediction

Predict multi-chain protein assemblies and compare interface geometry, stoichiometry assumptions, confidence, and model agreement.

Protein design

Compare protein-design tasks by what is being created, the evidence supplied, the model output, and the experiments needed next.

Protein structure alignment

Identify a plausible structural fold for a difficult protein sequence, then review candidate models and templates without hiding the external threading step.

Molecular dynamics simulation

Prepare a protein, run conventional GROMACS molecular dynamics, and retain trajectories, energies, settings, and structural analyses.

Protein structure prediction

Predict residue-level helices, strands, and coils from sequence, then compare them with coordinate-derived assignments.

Sequence alignment

Align amino-acid sequences with protein-aware methods and interpret conservation in structural and functional context.

Protein design

Generate or optimize amino-acid sequences against structural, functional, stability, and developability objectives.

Protein structure alignment

Choose pairwise comparison, database search, fold-recognition review, or multiple-structure review according to the evidence and output you need.

Protein structure prediction

Compare prediction methods by starting evidence, molecular system, output, confidence, and downstream research workflow.

Protein structure alignment

Search large protein-structure databases with a query fold, then inspect ranked neighbors, coverage, scores, and alignments.

Molecular docking

Generate and compare plausible small-molecule binding poses within a prepared protein target and defined search region.

Molecular docking

Model how two prepared protein structures may assemble and interact within a biologically plausible complex.

Molecular dynamics simulation

Review reconstructed replica trajectories while keeping exchange statistics and equilibrium claims anchored to the external ensemble.

RNA structure prediction

Generate and compare atomic RNA structure hypotheses with multiple biomolecular foundation models.

RNA structure prediction

Predict RNA base pairing, minimum-free-energy structures, alternative folds, and local accessibility from sequence.

RNA structure prediction

Choose the RNA prediction workflow that matches the biological question: intramolecular base pairing, atomic 3D coordinates, or intermolecular RNA binding.

RNA structure prediction

Compare joint folding, duplex hybridization, accessibility-aware binding, and fast query–target screening for two RNAs.

Sequence alignment

Choose the alignment scope that matches your evidence, then run a connected workflow with explicit inputs, settings, and outputs.

Virtual screening

Prepare reference ligands and candidate conformers, compare three-dimensional shape and chemical features, then review a diverse shortlist in one connected workflow.

Protein structure prediction

Predict three-dimensional protein structures directly from one sequence without supplying alignments, templates, or homologous sequences.

Molecular dynamics simulation

Review structures and compatible trajectories from steered simulations while keeping force, work, pathway, and protocol claims tied to the external run.

Sequence alignment

Use three-dimensional geometry to derive residue correspondence when sequence similarity alone is too weak or ambiguous.

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.

Protein structure prediction

Predict membrane-protein folds and examine hydrophobic segments, topology context, confidence, and explicit membrane-orientation limitations.

Virtual screening

Compare in silico screening approaches, then start an online workflow for compound preparation, ranking, review, and export.

Sequence alignment

Compare genome assemblies with coordinate-aware alignment, dot plots, variant tables, and retained delta files.