Overview
What this category covers
Simulation is how a static structure is tested against time. This category covers classical molecular dynamics for stability and mechanism, end-point free energy methods for ranking compounds within a series, and rigorous alchemical calculations where a synthesis decision justifies the cost. Replicates, convergence assessment and honest reporting of what the sampling supports are standard rather than optional.
What we deliver
▸All-atom simulation of protein, protein–ligand, membrane and nucleic acid systems
▸Trajectory analysis directed at your specific question rather than a generic plot panel
▸MM/GBSA and MM/PBSA ranking with per-residue energy decomposition
▸FEP and relative binding free energy calculations validated against your measured data
▸Convergence assessment and an explicit statement of what the simulation does not establish
Who this is for
▸Teams needing to know whether a docked pose is real
▸Lead optimisation programmes choosing between analogues before synthesis
▸Groups investigating resistance mutations or allosteric mechanism
▸Projects requiring publication-grade simulation support
How engagements in this category are run
Simulation projects are scoped from the question backwards: the process you need to observe determines the timescale, the replicate count and whether enhanced sampling is required. Setup is treated as the critical stage, since most misleading simulations originate in protonation, parameterisation or membrane composition rather than in sampling. Deliverables include the full input set, so the work can be extended or repeated by your team, and every study states what the sampling achieved and what it did not.
Services
3 computational services in this category
E1
Classical MD Simulation
All-atom MD of protein–ligand, protein–protein, protein–membrane systems (100 ns–10 µs). RMSD/RMSF/H-bond/contact map trajectory analysis.
Learn MoreE2
MM/GBSA & MM/PBSA Binding Free Energy
End-point free energy calculations from MD trajectories. Per-residue energy decomposition, hot-spot identification, compound ranking.
Learn MoreE3
Free Energy Perturbation (FEP / RBFE)
Rigorous alchemical FEP for precise compound ranking (±1 kcal/mol). Relative and absolute binding free energy for lead optimization.
Learn MoreIn Practice
What a project in this category looks like
Three shapes we are asked for most often. Scope is always set after a feasibility review, so timelines below are typical rather than quoted.
Testing whether a docked pose survives
The situation
Docking produced a plausible binding mode that the team is about to design around, and no experimental structure exists.
What we do
System preparation with careful protonation and parameterisation, replicate simulations of the complex, contact persistence and pose stability analysis, and convergence assessment across replicates.
What you receive
Trajectories with full inputs, pose stability metrics, the contacts that persist and those that do not, and an explicit statement of what the sampling supports.
Typical timeline: 2–4 weeks
Ranking analogues before synthesis
The situation
Ten to fifty analogues are on the drawing board and the chemistry team can only make a fraction of them.
What we do
Consistent simulation across the series followed by end-point free energy calculation with per-residue decomposition, benchmarked against any compounds already measured.
What you receive
A ranked table with component breakdown, the interactions carrying the binding, correlation against your measured data, and a note of which differences sit within noise.
Typical timeline: 2–4 weeks
Understanding a resistance mutation
The situation
A clinical or laboratory mutation has reduced compound activity and the team needs to know why before redesigning.
What we do
Simulations of wild-type and mutant systems with and without the compound, interface and dynamics comparison, and free energy calculation of the affinity change where the series supports it.
What you receive
A mechanistic account of what changed — lost contact, altered dynamics, shifted conformational preference — with the design implication stated.
Typical timeline: 3–6 weeks
Questions
Asked before we scope this work
How long should the simulation run?
Long enough for the process in question: side-chain motion needs nanoseconds, loop motion tens to hundreds, domain motion microseconds or enhanced sampling. We scope the length to the question, not to a default.
Will you tell us if the result is inconclusive?
Yes. Where replicates disagree or sampling has not converged, that is stated plainly rather than smoothed into an average.
Can we extend the simulations ourselves afterwards?
Yes. Complete inputs, topologies and parameters are delivered so your team can continue or repurpose the system without rebuilding it.
What Published Work Reports
The results below were published by independent groups and are cited to show what these computational approaches have achieved in the literature. They are not ICDMO project results, and outcomes vary substantially between targets, datasets and programmes. We do not promise comparable results for any particular project.
Alchemical free energy calculations reach roughly 1 kcal/mol error
Benchmark studies on congeneric series across multiple drug targets report root-mean-square errors around 1 kcal/mol, with published protocol work reporting prediction errors below approximately 1.3 kcal/mol on test sets of ligand transformations. An error of this size is small enough to separate compounds differing by roughly one order of magnitude in affinity, which is what makes the method useful for deciding which analogue to synthesise.
Protocol and benchmark studies, Scientific Reports, 2019 ↗Accuracy is system-dependent, and retrospective benchmarks flatter it
Reviews of free energy methods in drug discovery note that much of the published evidence is retrospective, and that prospective performance in live optimisation campaigns is less thoroughly documented. This is why we validate against your own measured compounds before issuing prospective predictions, rather than quoting a literature error bar as though it applied to your system.
Review, Free Energy Calculations for Drug Discovery, 2021 ↗More
Other service categories
Target Identification & Validation5Virtual Screening (Small Molecule)3Small Molecule Design & Optimization2ADMET & Drug-Likeness Prediction4AIDD — Small Molecule Platform2Structure-Based Drug Design (SBDD)3Bioinformatics & Multi-Omics Analysis11Antibody Design & Engineering (AI)5Peptide & Cyclic Peptide Drug Design4Protein Design & Engineering (AI)4ADC & Bioconjugate Design2Compound & Biological Library Design3
Bring us the scientific question, not a service code
Share your target, dataset, sequences or objective. We will recommend a scoped computational plan, the expected deliverables, a timeline and the validation options.
Request a Feasibility Review