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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 12 of 90 research services

Dynamics, free energy and enhanced samplingMolecular simulation

Molecular dynamics

Use time-evolution sampling to assess conformational stability, interaction occupancy and plausible mechanistic paths.

System setup, equilibration and production simulationConformation, contact and collective-motion analysisClustering, free-energy landscapes and replicate sampling
Primary deliveryInputs, parameters and trajectories
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Free-energy calculations

Select endpoint, absolute or relative free-energy strategies according to system similarity, budget and precision goals.

MM/GBSA and MM/PBSAPer-residue energy decompositionABFE, RBFE and FEP
Primary deliveryFree-energy estimates with uncertainty
Dynamics, free energy and enhanced samplingMolecular simulation

Membrane-protein and biomembrane modelling

Construct membrane environments with lipids, ions, ligands and glycosylation to study membrane-protein conformations and interfaces.

Membrane placement, lipid composition and system setupIon, cofactor and post-translational-modification parameterisationMembrane thickness, tilt, contacts and hydration analysis
Primary deliveryComplete membrane system with parameter records
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Enhanced sampling and conformational free energy

Select collective variables and sampling strategies for high barriers and rare conformations, comparing transitions and relative free energies.

Metadynamics and umbrella samplingREST2, accelerated dynamics and path samplingReweighting, uncertainty estimation and collective-variable diagnostics
Primary deliverySampling protocol and bias records
Dynamics, free energy and enhanced samplingMolecular simulation

Competitive binding simulation

Compare interface contacts, conformational states and approximate energetic trends under matched conditions with and without a competitor to form a testable competition hypothesis.

Matched-condition complex constructionMolecular dynamics and interface-contact analysisMM/GBSA and free-energy-landscape review
Primary deliveryMatched systems and parameter records
Dynamics, free energy and enhanced samplingMolecular simulation

All-atom molecular dynamics

Track biomolecules, ligands, solvent and ions at atomic resolution to analyse reproducible structural and interaction trends.

System parameterisation and equilibrationReplicate all-atom simulationsConformational, contact and dynamic analysis
Primary deliveryComplete systems and trajectories
Dynamics, free energy and enhanced samplingMolecular simulation

Coarse-grained molecular dynamics

Reduce degrees of freedom to access larger scales for membranes, self-assembly, polymers and large complex systems.

Mapping and parameter selectionCoarse-grained system assembly and simulationCluster, morphology and back-mapping review
Primary deliveryCoarse-grained models and trajectories
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Umbrella sampling and PMF

Place overlapping windows along a defined reaction coordinate to reconstruct a relative potential of mean force with overlap and convergence checks.

Reaction-coordinate and window designRestrained sampling and overlap checksWHAM or MBAR reconstruction and uncertainty assessment
Primary deliveryWindow trajectories and histograms
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Steered molecular dynamics

Apply controlled external forces along defined directions to compare dissociation paths, mechanical response and follow-up free-energy windows.

Pulling-direction and restraint designReplicate steering at selected ratesForce–extension and pathway-structure analysis
Primary deliveryControlled-path trajectories
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Replica-exchange molecular dynamics

Expand conformational sampling through temperature- or Hamiltonian-space replica exchange for peptides, folding units and multistable systems.

Replica and exchange-dimension designParallel sampling and exchange monitoringReweighting and state-population analysis
Primary deliveryReplica trajectories and exchange logs
Dynamics, free energy and enhanced samplingEnhanced sampling and free energy

Targeted molecular dynamics

Apply progressive restraints between known start and target structures to generate candidate transition paths and locate possible structural bottlenecks.

End-state alignment and restraint-region selectionMultiple targeted simulationsPath clustering and contact-change analysis
Primary deliveryCandidate transition paths
Dynamics, free energy and enhanced samplingMolecular simulation

Antibody molecular dynamics

Compare antibody conformational stability and local flexibility around CDRs, frameworks, antigen interfaces and optional glycosylation states.

Antibody numbering and system preparationReplicate all-atom simulationsCDR, interface and clustering analysis
Primary deliveryAntibody systems and trajectories
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