Molecular Docking
Protein–ligand docking & interaction analysis
Receptor and ligand preparation, binding-site grid setup, redocking validation where supported, pose ranking, 2D/3D interaction diagrams, and methods report.
Computational Chemistry & Molecular Simulation
Molecular docking and molecular dynamics, carefully executed and clearly reported.
ReactorMD provides structure preparation, protein–ligand docking, GROMACS molecular dynamics simulations, and trajectory analysis for students, PhD researchers, and academic laboratories. Every project is delivered as a reproducible research package with publication-ready figures, documented methodology, and organized coordinate files.
- $0.99
- Molecular docking · up to 10 ligands
- $8.00
- 25 ns Apo MD · Complex MD from $15.00
- Complete ZIP
- Methods report, figures & raw files
Illustrative Complex · Chain A (371 aa) + Bound Inhibitor (LIG)
From raw structure to organized report in one traceable workflow
Every simulation and docking project follows documented preparation, validation, and post-processing steps. Final workflow parameters depend on the biological target, force field, system composition, and agreed project scope.
Target Inspection
Evaluate PDB/mmCIF resolution, missing loops, alternate conformations, and co-crystallized ligands.
Structure Preparation
Assign protonation states, repair side chains, standardize ligand tautomers, and minimize 3D geometries.
Molecular Docking
Define binding-site grid coordinates, validate by redocking where reference ligands exist, and rank poses.
Complex Assembly
Combine top-ranked protein–ligand poses with consistent ligand parameterization and topology checks.
System Solvation
Construct periodic boundary boxes, solvate with explicit water, and neutralize with physiological counter-ions.
Equilibration & MD
Execute steepest-descent energy minimization, restrained NVT/NPT equilibration, and unrestrained production MD.
Trajectory Analysis
Compute RMSD, RMSF, radius of gyration, SASA, H-bond occupancy, PCA, and free-energy landscapes.
Organized Delivery
Package high-resolution plots, structure files, parameter logs, and a transparent methods report in one ZIP.
Computational services scoped for academic and laboratory research
Select a workflow below to configure ligand counts, simulation durations, and input files, or read the technical service documentation first.
Molecular Dynamics
GROMACS simulation + full trajectory analysis
System topology building, solvation, energy minimization, NVT/NPT equilibration, production MD (25–500 ns), and RMSD, RMSF, Rg, SASA, H-bond, PCA & FEL analysis.
Homology Modelling
Sequence-to-structure 3D protein modelling
Sequence review, template search and alignment, 3D structural model generation, Ramachandran and clash assessment, and documented structural limitations.
Ligand Preparation
Compound library standardization & 3D prep
Structure checking, salt stripping, protonation and tautomer state assignment, 3D coordinate generation, energy minimization, and format conversion (SDF/MOL2/PDBQT).
Computational ADME
Physicochemical & drug-likeness prediction
Molecular descriptors, Lipinski/Veber/Egan filters, solubility and permeability estimates, medicinal chemistry alerts, and transparent model limitation notes.
2D QSAR Modelling
Supervised structure–activity relationship models
Dataset curation, 2D molecular descriptors, feature selection, train/test splitting, R²/Q²/RMSE validation, applicability domain mapping, and activity prediction.
Virtual Screening
High-volume compound library screening
Docking-based prioritization of 500 to 10,000+ compounds with ranked hit lists, docked pose archives, and top-hit interaction summaries.
Trajectory Analysis
Post-processing for existing MD trajectories
Already have XTC/TRR/DCD trajectories and topology files? Order standalone RMSD, RMSF, Rg, SASA, H-bond, PCA, FEL, or MM/PBSA post-processing.
Not sure which computational workflow fits your research question?
Answer three quick questions in the guided project assistant to match your starting files and research goal with the right service.
Technical Specifications
Detailed workflow documentation for every service
Review required input formats, step-by-step protocols, deliverables, and methodological limitations before submitting your files.
Structure-Based Docking
Protein–ligand molecular docking
Grid definition, redocking RMSD checks, pose scoring, and non-covalent interaction mapping.
Explicit-Solvent MD Molecular dynamics simulationGROMACS topology building, equilibration, production runs, and integrated trajectory analysis.
Chemical Standardization Ligand preparation workflowsProtonation states, tautomer enumeration, 3D conformation generation, and format conversion.
Comparative Modelling Protein homology modellingTemplate selection, sequence-structure alignment, loop building, and stereochemical validation.
Pharmacokinetic Profiling Computational ADME predictionLipinski, Veber, and physicochemical descriptor profiling with documented model applicability.
Statistical Modelling 2D QSAR modellingDescriptor calculation, feature selection, internal/external validation, and domain analysis.
Library Prioritization Virtual screening of compound librariesHigh-throughput docking, multi-step filtering, and traceable hit-list organization.
Conformational Post-Processing MD trajectory analysisRMSD, RMSF, radius of gyration, SASA, hydrogen bonding, PCA, clustering, and FEL plots.
End-State Energy Estimation MM/PBSA binding free-energy analysisSnapshot-based binding energy estimation and per-residue decomposition from MD trajectories.
Public Compound Subsets ZINC20 compound-library workflowsSubset selection, property filtering, and docking preparation for ZINC20 screening campaigns.
Molecular dynamics with trajectory analysis included
Every standard ReactorMD simulation package includes periodic boundary correction and trajectory post-processing so you receive interpretable figures alongside raw coordinate trajectories.
RMSD backbone & ligand stability
RMSF residue flexibility
Rg & SASA compactness & solvent exposure
PCA & FEL conformational states
Sample outputs from real computational workflows
Inspect representative figures and package structures generated by ReactorMD workflows. These examples are demonstration research outputs, not customer testimonials or experimental validation.
Standardized Packaging
What you receive with every completed order
01 · Inputs & Prep
Cleaned receptor structures, standardized ligands, and topology files.
02 · Trajectories
Processed coordinates, docked poses, or PBC-corrected MD trajectories.
03 · Quantitative Data
Tabular scores, CSV/XVG metric series, and interaction tables.
04 · Figures
High-resolution plots and structural renders ready for manuscripts.
05 · Methods Report
Documented software versions, parameters, and scientific limitations.
06 · Complete ZIP
Logically numbered directory archive downloadable from your account.
Verify your package price before submitting files
All standard tiers use fixed USD pricing from a single authoritative schedule. If a custom system requires additional work, ReactorMD requests your approval before any extra charge.
SELECTED PACKAGE ESTIMATE
$0.99
10 ligands
Up to 4 hours estimated turnaround.
Designed for students, PhD researchers, and academic labs
Whether you need a single docking validation for a dissertation chapter or multi-hundred-nanosecond GROMACS trajectories for a manuscript revision, workflows are structured for clarity and reproducibility.
Undergraduate & Master's thesis projects
Accessible starting prices from $0.99 with clear methods documentation suitable for thesis chapters and viva defense.
Manuscript & thesis studies
Protein–ligand MD, redocking validation, PCA/FEL landscapes, and MM/PBSA energy estimates with full parameter transparency.
Medicinal chemistry & biology groups
Prioritize synthetic or isolated compound series before wet-lab assays without maintaining dedicated GPU clusters.
Self-hosted workflow software
License ReactorMD Dock or ReactorMD MD when your laboratory prefers to execute pipelines on local workstation hardware.
Prefer to run workflows on your own hardware?
ReactorMD Dock and ReactorMD MD package our guided input preparation, live execution logs, and automated report generation into local desktop interfaces with 10 days of setup support.
ReactorMD Dock
Guided protein–ligand docking interface that automates structure preparation, grid-box configuration, pose ranking, and report export.
- Guided receptor and ligand input validation
- Real-time execution log and pose ranking table
- Automated interaction figures and ZIP export
- Installation guide + 10 days of setup support
ReactorMD MD
Streamlined GROMACS simulation runner covering topology preparation, solvation, NVT/NPT equilibration, production MD, and trajectory post-processing.
- Automated solvation, neutralization, and MDP setup
- Live simulation progress and energy monitoring
- Built-in RMSD, RMSF, Rg, SASA, and PCA plotting
- Installation guide + 10 days of setup support
Scientific Scope & Limitations
Reproducible pipeline automation—never unverified black-box claims.
01 · Transparent engines: Built around established computational chemistry tools and documented force fields.
02 · Predictive clarity: Docking scores and end-state energy estimates rank hypotheses; they do not replace experimental Ki/Kd or IC50 assays.
03 · Structured archives: Every local run exports raw logs, topologies, and publication-oriented plots in a standardized folder layout.
Educational Resource Library
Practical guides to molecular docking, GROMACS MD, and analysis
Clear, methodologically grounded tutorials written for students and researchers who want to understand the science behind each step.
Docking Tutorial
How to run molecular docking: step-by-step workflow
Receptor cleaning, ligand protonation, binding-site grid placement, redocking RMSD validation, and pose inspection.
GROMACS Workflow GROMACS protein–ligand MD simulation guideTopology assembly, explicit solvation, energy minimization, NVT/NPT equilibration, production MD, and PBC centering.
Trajectory Interpretation How to interpret RMSD, RMSF, Rg, SASA, and H-bondsEvaluate structural convergence, local loop flexibility, compactness, and persistent ligand interactions.
Binding Free Energy MM/PBSA binding free energy explainedHow end-state continuum solvation methods work, frame sampling best practices, and key approximations.
Pharmacokinetics ADME and Lipinski’s Rule of Five explainedPhysicochemical descriptors, oral bioavailability heuristics, and why drug-likeness rules are filters rather than guarantees.
Compound Screening Virtual screening workflow: from library to hit listLibrary curation, property pre-filtering, control docking validation, pose clustering, and hit selection.
Built on practical structure preparation, GROMACS simulation, and organized reporting
ReactorMD was created to make reproducible molecular modelling workflows accessible to students, doctoral candidates, and research laboratories that need dependable execution without command-line bottlenecks.
All outputs delivered by ReactorMD are computational predictions intended to guide research hypotheses and must be distinguished from experimentally confirmed biological or clinical findings.
Documented parameters
Reproducible GROMACS & docking workflows
Transparent USD pricing
Authenticated private file handling
Sohel Akhtar Ansari is the founder of ReactorMD and a computational drug discovery researcher. His work focuses on computational antitubercular drug discovery, protein–ligand molecular docking, GROMACS molecular dynamics simulations, ligand preparation, 2D QSAR modelling, virtual screening, and reproducible scientific data analysis.
Common questions about workflows, files, and pricing
What files do I need to provide for molecular docking?
Typically a receptor structure (PDB or mmCIF format, or a RCSB PDB identifier) and ligand structures (SDF, MOL2, MOL, or SMILES). If your target structure is only available as an amino-acid sequence, ReactorMD can route your project to homology modelling first.
Does the molecular dynamics service include trajectory analysis?
Yes. Standard GROMACS molecular dynamics packages include trajectory processing and the supported analysis suite—including RMSD, RMSF, radius of gyration (Rg), solvent-accessible surface area (SASA), hydrogen-bond analysis, principal component analysis (PCA), and free-energy landscapes (FEL).
Does a favorable docking score prove that a compound binds experimentally?
No. Molecular docking provides a computational prediction of binding pose and relative ranking. Scores should always be interpreted alongside structural inspection, molecular dynamics stability checks, and experimental biochemical assays.
What does a 25 ns or 100 ns simulation duration mean?
It refers to the physical timescale simulated during the unrestrained production phase of the molecular dynamics trajectory under the selected force field and solvent conditions.
What input data is required for 2D QSAR modelling?
Supervised 2D QSAR requires a curated dataset of chemical structures paired with consistent experimental biological activity or property measurements (such as IC50, Ki, or logS values).
What happens if my project requires custom preparation or scope changes?
If your uploaded structures require non-standard parameterization or custom scope beyond the selected package, ReactorMD will explain the technical requirements and obtain your approval before any additional charges apply.
How are my research files stored and delivered?
Uploaded scientific inputs and final deliverables are stored outside the public web root and linked to your authenticated ReactorMD account. Only you and authorized administrative staff can access your project package.
Which payment methods are supported?
Checkout supports server-verified transactions through PayU and PayPal in USD, while custom-scope projects use the no-obligation quotation workflow.
Contact & Custom Scope
Questions, custom simulation lengths, or thesis/publication support?
Send us your target details, compound count, or custom simulation requirements. Custom-scope enquiries are reviewed manually before any payment is requested.
Direct Public Contact
Email: info@reactormd.com
For existing orders, include your
Email: info@reactormd.com
For existing orders, include your
RMD- order reference.
SERVER-VERIFIED CHECKOUT (PAYU & PAYPAL)
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PRIVATE RESEARCH FILE STORAGE
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REPRODUCIBLE METHODS REPORTS