SimDock Lab
Docking & MD Simulation Request Portal
⚗️ SimDock Lab Docking free • MD via server
Submit docking & MD jobs in minutes, not days.
SimDock Lab is a lightweight web portal that standardizes molecular docking and GROMACS-based molecular dynamics workflows. Configure jobs, upload PDBs, generate Job IDs, and get everything routed to our compute backend with email confirmations for you and the support team.
No installation • No command line • Just upload, submit and track via Job ID.
Module 1
Free Molecular Docking Server
Submit protein–ligand, protein–protein, protein–peptide or ligand–ligand docking jobs at zero cost. Job IDs and all input files are sent to support@simdocklab.in for backend processing.
Module 2
MD Simulation Server (GROMACS)
Set up protein–ligand, apo, membrane, steered MD and other simulation types with version-controlled GROMACS, force-field selection, trajectory analyses and optional advanced post-processing workflows.
Workflow
Job ID, Email & Status Tracking
Each submission generates a unique Job ID. Confirmation emails go to you and the SimDock Lab support mailbox. Use the Job ID later to follow up or check status through the portal or by mail.

Where SimDock Lab fits in your workflow

SimDock Lab sits between your scientific question and heavy compute. It gives you a standardized way to request molecular docking and MD simulation jobs for research, service and training — without asking every student or collaborator to learn low-level Linux and scripting.

For research projects

Use the free docking module to quickly screen phytochemicals, FDA-approved drugs or in-house ligands against your target. Once promising complexes are identified, move to the MD Simulation Server to study stability, key interactions, and mechanistic behaviour across 100–1000 ns.

For services & CRO work

Treat SimDock Lab as your intake portal: every external request comes with a Job ID, structured metadata and attached PDB files, so your team can directly run docking or MD pipelines on internal workstations or clusters and then report back cleanly.

For training & marketing

In workshops and marketing campaigns, you can showcase SimDock Lab as a live gateway for structure-based drug discovery: participants submit real docking or MD jobs, receive Job IDs, and later see the analysis as figures and plots that can go into posters, theses or manuscripts.

SimDock Lab does not perform the calculations in your browser. Instead, it acts as a structured gateway: you define your systems and upload files here; the backend team runs docking and MD simulations on dedicated workstations or clusters and shares the analysis through email and secure links.

Molecular Docking (FREE)

Submit protein–ligand, protein–protein, protein–peptide or ligand–ligand docking jobs. Docking is currently provided as a free service; only valid metadata and files are required.

Docking request
Specify docking category, system size and upload your input files
Docking cost: INR 0
Upload PDB & docking input files
Upload receptor, ligands, grid boxes, and parameters.
📁
Click to browse or drag & drop files here
PDB, MOL2, SDF, config / text files · Max 10 files · 10 MB each
Job ID generated on submit

Docking summary

Docking category Protein–ligand docking
Ligands 1
Proteins 1
Docking pairs (lig × prot) 1
Docking cost INR 0 (FREE)
Files attached 0
Check Docking Job Status
Enter your docking Job ID to check status (requires backend implementation).
In production, this will query /api/job-status?jobId=... and display live information.

MD Simulation Server (GROMACS)

Configure molecular dynamics simulations with controlled GROMACS versions, force fields, water models, trajectory analysis and advanced post-processing. Suitable for protein–ligand, apo, membrane, steered and protein–protein systems.

MD Simulation request
Enter ns length, dynamics category, system size and analysis needs
MD billed via bank transfer
Upload PDB / topology / trajectory files
Upload the structures and inputs for MD setup or continuation.
📁
Click to browse or drag & drop files here
PDB, GRO, TOP, ITP, MDP, XTC/TRR · Max 10 files · 10 MB each
GROMACS configuration
Select version, force field, box, water model and basic trajectory analyses.
These standard analyses (RMSD, RMSF, Rg, SASA, H-bonds) are included at no extra charge.
MMPBSA analysis is currently supported only for jobs using GROMACS 2019.
Additional analysis (optional, ₹1,000 each)
Each selected analysis adds INR 1,000 to the MD subtotal.










Job ID & bank details sent via email after submission

MD summary

Dynamics category Protein–ligand simulation
MD base unit price INR 3,000
Number of MD runs 1
Extra analyses selected 0
Extra analysis subtotal INR 0
MD subtotal (incl. extra analysis) INR 3,000
Subtotal (before GST) INR 3,000
GST (18%) INR 540
Grand total INR 3,540
Files attached 0
Payment information
After submission, you will receive an email with:
  • Your Job ID
  • Bank transfer details
  • Instructions to share payment screenshot
Bank (for MD jobs):
ICICI Bank, SRNOME Private Limited, A/C: 233105001695, IFSC: ICIC0002331, Branch: Bangalore
Check MD Job Status
Enter your MD Job ID to see status (requires backend implementation).
In production, this will query /api/job-status?jobId=... and display live information.

Terms & Conditions

Please read these carefully before submitting any docking or MD simulation request through SimDock Lab.

Docking service

  • Docking service is currently offered free of charge; SimDock Lab reserves the right to revise pricing in future without prior notice.
  • Jobs are processed in a queue; turnaround time depends on complexity and current load. No fixed delivery date is guaranteed.
  • Docking results are strictly for research and educational use and must not be used for clinical decision making.
  • You are responsible for the correctness of the input structures, sequences, and identifiers you upload.
  • By submitting files, you confirm you have the rights or permissions to use and share the data with the SimDock Lab team.
  • Confidential or unpublished data will be treated as confidential and used only for performing the requested analysis; an NDA is recommended for highly sensitive projects.
  • SimDock Lab is not liable for any decisions, claims, or losses arising from the interpretation or downstream use of the docking results.
  • Very large systems or special workflows may require a custom quotation and may not be covered under the free tier.

MD simulation service

  • All MD work is executed only after confirmation of payment against the communicated quotation or agreed scope.
  • Protein systems with > 500 amino acids may require revised timelines and resources based on internal evaluation.
  • Each additional analysis option (PCA, FEL, MMPBSA, KDE, etc.) may be quoted separately depending on system size and complexity.
  • MMPBSA / binding free energy calculations are offered only when GROMACS 2019 is selected or explicitly agreed upon with the analysis team.
  • Turnaround time depends on system size, ns length, queue load, and selected analyses; no fixed delivery date is guaranteed unless confirmed in a formal email or work order.
  • Results are intended for research and educational use only and must not be used for diagnosis or direct clinical decision making.
  • You are responsible for verifying the correctness of all input structures, topologies, and parameters shared through the portal.
  • SimDock Lab and its operators are not liable for any indirect, incidental or consequential loss arising from the use or misinterpretation of the simulation results.

Communication & email

  • By clicking “Submit docking job” or “Submit MD job”, you agree to these terms and consent to receive emails related to quotations, invoices, simulation updates and result delivery.
  • Once you submit a job, an automated email with your Job ID (and for MD, bank transfer details) will be sent to your email and mirrored to support@simdocklab.in for internal tracking.
  • If you do not receive an email within a reasonable time, contact support@simdocklab.in with your Job ID for manual verification.

Contact Us

For queries, collaboration ideas, or custom workflows, drop us a line.

Email: support@simdocklab.in

Please include your Job ID (if you already submitted a request), your institute or company name, and a short description of what you need (docking, MD, or combined analysis).

This portal focuses on job collection and quoting. Actual processing, invoicing and data sharing are handled directly by the backend service team via email and secure file links.