HESUAN科研计算
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RESEARCH SERVICES

Find a computational service by research question

Browse eight research areas, focused topics or keywords to review method choices, input requirements, quality controls and concrete deliverables.

Showing 15 of 90 research services

Docking and target interactionsSmall-molecule docking

Small-molecule–protein docking

Evaluate plausible small-molecule binding poses and interactions across protein pockets, ligand microstates and conformational sampling.

Receptor-ensemble and ligand-microstate preparationSite-constrained docking and conformational samplingRescoring, pose clustering and interaction review
Primary deliveryCandidate binding poses and clusters
Docking and target interactionsMacromolecular and complex-partner docking

Peptide–protein docking

Explore plausible binding modes for flexible peptides using peptide ensembles, receptor interfaces and available restraints.

Peptide conformation and cyclisation/modification modellingFlexible docking with experimental restraintsInterface refinement, hotspot and pose-cluster analysis
Primary deliveryPeptide–protein complex pose ensemble
Docking and target interactionsMacromolecular and complex-partner docking

Protein–protein docking

Combine global or local search, conformational ensembles and interface evidence to propose testable protein-complex assemblies.

Global/local rigid-body and ensemble dockingIntegration of crosslink, mutation and coevolution restraintsInterface refinement, clustering and energy decomposition
Primary deliveryComplex pose clusters and interface ranking
Docking and target interactionsMacromolecular and complex-partner docking

Antigen–antibody docking

Build candidate antigen–antibody recognition modes around CDR conformations, antigen epitopes and experimental evidence.

Antibody numbering, CDR and structure-quality assessmentEpitope-guided ensemble dockingInterface refinement, paratope/epitope and developability review
Primary deliveryCandidate antigen–antibody complex poses
Docking and target interactionsMacromolecular and complex-partner docking

Nucleic-acid–protein docking

Explore candidate nucleic-acid–protein interfaces while explicitly considering DNA/RNA conformation, charge and known recognition sites.

Nucleic-acid conformation, ionisation and structure-quality assessmentRestraint-guided ensemble dockingInterface refinement and base/residue contact analysis
Primary deliveryCandidate nucleic-acid–protein complex models
Docking and target interactionsInterface and interaction analysis

Metal–protein docking

Assess candidate metal-binding modes using oxidation state, coordination geometry, protein protonation and site evidence.

Metal oxidation-state, donor-atom and protonation modellingCoordination-constrained site search and dockingGeometry review with QM/MM or parameter-sensitivity assessment
Primary deliveryCandidate coordination geometries and site ranking
Docking and target interactionsSmall-molecule docking

Fully flexible docking

Expand ligand and receptor side-chain/backbone sampling for systems with possible induced fit or multi-conformation recognition.

Receptor ensembles and flexible-region definitionCoupled ligand–receptor conformational samplingInduced-fit refinement and replicate comparison
Primary deliveryJoint receptor–ligand pose clusters
Docking and target interactionsSmall-molecule docking

Covalent docking

Build reaction-aware covalent-complex hypotheses around the warhead, protein nucleophile and non-covalent pre-complex.

Nucleophile, protonation and warhead definitionNon-covalent pre-docking and covalent-pose generationReaction-geometry, pose and off-target-risk review
Primary deliveryCandidate covalent binding poses
Docking and target interactionsSmall-molecule docking

Reverse target screening

Start from an anonymized small molecule and combine pocket-representation retrieval, structure preparation, batch docking and functional evidence to reduce the target-validation space.

Protein-pocket and ligand-representation retrievalStructure preparation, batch docking and distribution reviewCross-layer evidence intersection and functional enrichment
Primary deliverySource-traceable target tiers
Docking and target interactionsInterface and interaction analysis

Molecular docking and SAR interpretation

Relate activity changes in a congeneric series to candidate poses, substituent vectors and local environments to form testable SAR explanations.

Consistent series preparationConstrained docking and pose alignmentActivity-cliff and interaction-fingerprint analysis
Primary deliveryAligned series poses
Docking and target interactionsInterface and interaction analysis

Residue-interaction and hotspot analysis

Combine interface geometry, contact occupancy, energy decomposition and conservation to locate regions that may influence binding or recognition.

Interface contacts and buried areaComputational alanine scanning or energy decompositionCross-review with conservation and trajectory occupancy
Primary deliveryTiered hotspot residues
Docking and target interactionsInterface and interaction analysis

AlphaFold model docking-readiness assessment

Review local confidence, pocket geometry, conformational state and template support to decide which predicted regions are suitable for docking.

Confidence and error-map reviewPocket and key-residue geometry assessmentTemplate, state and refinement-needs evaluation
Primary deliveryUsable regions and risk flags
Docking and target interactionsMacromolecular and complex-partner docking

Small-molecule–DNA/RNA docking

Consider nucleic-acid conformation, charge, grooves and base stacking when exploring candidate small-molecule recognition modes for DNA or RNA.

Nucleic-acid and ionic-environment preparationSite-directed or blind dockingStacking, hydrogen-bond and electrostatic review
Primary deliveryCandidate binding poses
Docking and target interactionsMacromolecular and complex-partner docking

Carbohydrate–protein docking

Account for ring conformations, glycosidic torsions and hydroxyl networks when comparing oligosaccharide, glycan or glycomimetic binding modes.

Ring and linkage-conformer preparationEnsemble docking and pose clusteringHydrogen-bond, water-network and aromatic-stacking analysis
Primary deliveryCarbohydrate pose clusters
Docking and target interactionsInterface and interaction analysis

Enzyme–small-molecule interaction modelling

Compare candidate recognition modes for substrates, inhibitors or modulators around catalytic states, access channels, cofactors and protonation.

Catalytic-state and cofactor preparationSubstrate or inhibitor dockingChannel, catalytic-geometry and key-residue analysis
Primary deliveryCandidate recognition poses
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