Computational Biology · Service

Molecular Dynamics and
AI-Driven Design

From first principles to function — rigorous simulations that answer the questions your experiments alone cannot.

Your experiment tells you what happens. Our simulations tell you why. We run end-to-end MD simulations for academic groups, graduate students, and industry teams — from a single-protein thesis chapter to multi-compound drug discovery pipelines. Every project is built on validated protocols, reproducible workflows, and results you can publish.

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Capabilities

What We Simulate

Protein Systems

Apo Protein Dynamics

We map your protein's intrinsic flexibility, domain motions, and conformational landscape. Know the baseline before you interpret binding data or mutation effects.

Protein–Ligand Complexes

All-atom simulations of your drug–target, substrate–enzyme, or inhibitor–protein complex. We assess pose stability, residence time, key contacts, and the energetics driving recognition.

Protein–Protein Interactions

Simulations of homodimeric, heterodimeric, and multimeric assemblies. We characterize interface stability, cross-chain contact networks, and allosteric communication pathways between subunits.

Mutant and Variant Analysis

Wild-type vs. mutant, side by side. We quantify the structural and dynamic consequences of point mutations, insertions, or deletions — giving you the mechanistic evidence for rational design and variant interpretation.

Molecular Docking and Virtual Screening

Structure-Based Docking

Rigid and flexible docking of small molecules, peptides, and fragments against protein targets. Pose prediction, scoring, and consensus ranking across multiple docking programs.

Ensemble Docking

We dock against MD-derived conformational ensembles, not a single crystal structure. This captures induced-fit effects and cryptic binding sites that static structures miss entirely.

AI-Based Molecular Docking

Generative model-based docking that predicts binding poses without conventional search-and-score. Ideal for blind docking where the binding site is unknown. We use it alongside physics-based methods for better pose diversity and stronger consensus.

Post-Docking MD Validation

Short MD runs on top-ranked docking poses to filter false positives, confirm pose stability, and refine binding modes — before committing to longer, costlier simulations.

Polymer and Biomaterial Simulations

Cellulose and Lignocellulosic Systems

All-atom simulations of cellulose microfibrils, lignin oligomers, and cellulose–lignin composites. We study structural rigidity, solvent accessibility, enzymatic degradation surfaces, and pretreatment effects.

Synthetic and Natural Polymers

Simulations of polymer chains, blends, and assemblies (e.g. natural rubber), characterizing chain flexibility, radius of gyration, glass transition behavior, and intermolecular packing.

Advanced Simulation Methods

Free Energy Perturbation (FEP) and Thermodynamic Integration (TI)

Alchemical free energy calculations for quantitative prediction of relative binding affinities, solvation free energies, and mutation-induced stability changes. The gold standard when you need numbers, not just trends.

Enhanced Sampling

Metadynamics, replica exchange (REST2/REMD), and accelerated MD for systems trapped in local minima. Essential for studying slow conformational transitions, folding events, and rare binding/unbinding pathways.

Coarse-Grained Simulations

Martini and related CG models for studying large-scale membrane dynamics, protein aggregation, polymer self-assembly, and systems that exceed all-atom timescale limitations.

QM/MM Hybrid Methods

Quantum mechanical treatment of reaction centers within a classical MD environment. For enzymatic mechanisms, electron transfer, and systems where bond breaking is at the heart of your question.

AI-Driven Molecular Design

Structure Prediction and Ensemble Generation

AlphaFold and ColabFold for high-confidence structure prediction. ESM-2 for sequence-based structural and functional annotation. AI-predicted structures serve as starting points for MD validation and refinement.

De Novo Protein and Molecular Design

RFdiffusion for generative protein backbone design. REINVENT4 for de novo small molecule generation and lead optimization guided by multi-parameter objectives.

AI-Guided Binding Prediction

DiffDock for deep learning-based molecular docking. Integration of ML-interatomic potentials (ANI-2x, DeePMD-kit) for accelerated energy evaluations and hybrid simulation workflows.

Outputs

Analysis and Deliverables

Every project gets a tailored analysis package — the specific metrics that answer your question, not a generic folder of plots. Every deliverable goes directly into your manuscript, thesis, or technical report.

What We Analyze

Structural Stability and Flexibility

  • RMSD: system equilibration and structural drift
  • RMSF: per-residue flexibility profiles
  • Radius of gyration: overall compactness and structural expansion or collapse
  • Center of mass (COM) tracking: domain separation, subunit movements, and ligand displacement monitoring

Binding and Interaction Analysis

  • Hydrogen bond occupancy and lifetime analysis
  • Salt bridge tracking: formation, persistence, and occupancy across trajectories
  • Hydrophobic contact analysis
  • Interface SASA (solvent-accessible surface area)
  • Key distance monitoring (e.g., catalytic dyad/triad distances, cross-chain contacts)
  • Contact maps: residue-residue contact frequency and interaction persistence across simulations
  • Binding statistics: interaction fingerprints and binding mode characterization

Energetics

  • MM-PBSA / MM-GBSA binding free energy estimation
  • Per-residue energy decomposition: identifying residues driving binding
  • Linear Interaction Energy (LIE): rapid binding free energy estimation from electrostatic and van der Waals contributions
  • FEP/TI relative binding free energy calculations (where applicable)

Conformational Landscape

  • Principal Component Analysis (PCA): dominant motions and conformational substates
  • Covariance analysis: correlated atomic displacements underlying functional motions
  • Dynamic Cross-Correlation Maps (DCCM): correlated and anti-correlated residue motions
  • Clustering analysis: representative conformations from trajectory ensembles
  • Free energy landscapes from enhanced sampling

Network and Communication Analysis

  • Protein Structure Networks (PSN): residue interaction networks revealing communication pathways, hub residues, and allosteric connectivity
  • Allosteric communication pathway identification
  • Domain hinge analysis

Solvent and Distribution Analysis

  • Radial Distribution Function (RDF): solvent shell structure, ion distribution, and molecular pair correlations around sites of interest

What You Receive

01

Simulation Summary Report

System setup details (force field, box dimensions, ion concentration, equilibration protocol), production run parameters, and quality control metrics.

02

Analysis Report

Publication-quality figures with clear annotations, statistical analysis, and interpretation tied to your specific scientific question. For academic clients, written to be directly insertable into a methods/results section. For industry clients, formatted as a structured technical report.

03

Raw Data Package

Topology files, representative trajectory frames (or full trajectories upon request), and a detailed methods summary for reproducibility.

04

Methods Text

A ready-to-use methods section drafted for your manuscript, thesis, or internal documentation, with appropriate citations for force fields, software, and analysis protocols.

Technical Stack

Tools and Platforms

Every project is executed on industry-standard and state-of-the-art platforms, ensuring reproducibility and methodological rigor.

Simulation Engines

AMBER GROMACS NAMD OpenMM

Force Fields

ff19SB CHARMM36m GLYCAM_06j Lipid21 LignAmb25 GAFF2

System Preparation

PDB2PQR Packmol tleap CHARMM-GUI Antechamber parmchk2

Docking and Screening

AutoDock Vina DiffDock

AI / ML Tools

AlphaFold ColabFold ESM-2 RFdiffusion REINVENT4 ANI-2x DeePMD-kit

Visualization and Analysis

CPPTRAJ MDAnalysis PyMOL VMD ChimeraX
Process

How We Work

A structured, transparent process from your first message to the final figure: every decision documented and every output explained.

01

Consultation and Scope Definition

You share your question — a paper you are writing, a hypothesis to test, a reviewer's request. We define the strategy together: what system, what method, what timescale, and exactly which analyses will answer it.

02

System Preparation

We build, parameterize, and validate your system from scratch — structure curation, protonation states, force field selection, solvation, ionization, energy minimization. Every setup decision is documented and justified before a single simulation step is run.

03

Production Simulations

Simulations run on GPU-accelerated HPC infrastructure. We run a minimum of three independent replicates for statistical robustness. Convergence and quality are monitored throughout — not just checked at the end.

04

Analysis and Interpretation

We do not hand you a folder of plots. Every figure is interpreted in the context of your biology. If the data points to a follow-up simulation or a better approach — we tell you.

05

Delivery and Post-Delivery Support

You receive the full package: report, figures, raw data, and publication-ready methods text. We stay available through peer review — revision requests, reviewer responses, and follow-up analyses included.

Pricing

Standard Packages

Four tiers to match your scope — a thesis chapter, a comparative study, an integrated design pipeline, or ongoing support. Every package includes raw data, reproducible scripts, and post-delivery support through publication. Pricing on consultation.

Starter

Single System MD

Best for: A lab or graduate student that needs one protein or complex simulated to support a paper or thesis chapter.

  • System preparation and parameterization (1 system)
  • 3 × 100 ns production replicate simulations
  • Analysis suite selected as needed to answer your specific scientific question
  • Analysis report with publication-quality figures
  • Methods section for manuscript or thesis
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Standard

Comparative MD

Best for: Wild-type vs. mutant, apo vs. bound, or ligand comparison studies.

  • System preparation for 2–3 related systems
  • 3 × 200–300 ns replicates per system
  • Comprehensive analysis suite with comparative analysis as needed for the scientific question
  • Binding free energy estimation where applicable
  • Comparative report with statistical evaluation
  • Methods section and reviewer response support
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Advanced

Integrated Simulation and Design

Best for: Projects requiring advanced sampling, free energy calculations, or AI-driven design components.

  • Everything in Standard, plus:
  • Enhanced sampling or alchemical free energy calculations
  • AI-based structure prediction or docking
  • Extended timescales or large-scale ensemble simulations
  • Multi-method validation pipeline
  • Full project report with integrated interpretation
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Custom

Ongoing Support

Best for: Labs or companies that need a computational collaborator on an ongoing basis.

  • Flexible scope: monthly retainer or per-project pricing
  • Priority scheduling and dedicated support
  • Co-authorship arrangements where appropriate (academic)
  • Confidential deliverables under NDA (industry)
  • Suitable for multi-paper projects and drug discovery pipelines
  • Teams building internal computational capacity
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FAQ

What to Expect

A single-system project (Starter package) typically takes 2–4 weeks from system setup to final report, depending on system complexity and simulation timescale. Comparative studies take 4–6 weeks. Projects involving enhanced sampling or FEP may require 6–8 weeks.
Yes. We routinely work with homology models, AlphaFold predictions, and cryo-EM structures. We assess model quality and apply appropriate validation before simulations. If your structure has gaps or unresolved regions, we handle the reconstruction.
We offer analysis-only services. If you or your collaborator have already run simulations, send us the trajectories and we will perform the analysis and generate publication-ready outputs.
That is the explicit goal. For academic clients, every deliverable (figures, analysis, and methods text) is designed to go directly into a manuscript or thesis. We also support reviewer response if computational methods are questioned during peer review. For industry clients, deliverables are formatted as internal technical reports with the same rigor and detail.
For academic projects involving substantial intellectual contribution (experimental design, interpretation, and manuscript writing), co-authorship is discussed upfront and follows standard academic norms. For straightforward service work, acknowledgment is sufficient. For industry clients, all work is delivered under service agreements with full IP clarity. Terms are agreed before work begins.
Yes. For industry and commercial clients, we work under NDAs and maintain strict confidentiality of all proprietary structures, sequences, and results. For academic clients, we follow standard collaborative norms and do not share data outside the project.
At minimum: your scientific question, the relevant structure(s) (PDB ID, file, or sequence), and any specific conditions or variables you want tested. We handle everything else.
We offer flexible pricing for student projects and understand the budget constraints of academic work. A focused Starter package for a thesis chapter is significantly more accessible than you might expect. Reach out and we will work something out.
Absolutely. This is one of our most common project types. Reviewers requesting MD validation, additional replicates, or specific analyses is exactly the kind of work we handle quickly and efficiently.
Yes. We routinely work under NDAs and can deliver results as confidential technical reports without any public disclosure. Timelines and deliverables are scoped to match your R&D milestones.
Get Started

Ready to Simulate?

Have a structure to simulate? A binding question to answer? A reviewer asking for MD data? Send us your question — we will design the simulation strategy and deliver results you can publish.

Discuss Your Project

Typical response time: 48 hours. Student projects, academic labs, and industry R&D all welcome.