Services

Here at RxTx, we offer software development services and high-throughput virtual screening protocols that will enable and accelerate your drug discovery and development efforts and/or academic basic research. We also provide services of equipping your lab using RxTx workflows and continued IT and scientific support.

Software Development, Integration, and Deployment

This docking software I use is great. If only it had this feature I just read about in a paper implemented in its code!

A modular and lightweight form of RxDock and the extended suite we use allows for customization of the software and implementation of new features. Our services as software developers include:

  • Add a new feature, e.g. develop a new module for RxDock that implements a particular method
  • Improve existing functionality, e.g. customize the existing code in RxDock for solving a particular problem
  • Extend the RxDock API for your particular requirements
  • Fix a particular issue in RxDock as soon as possible
  • Integrate RxDock into your workflow or automate your workflow that uses RxDock

High-Throughput Virtual Screening

High-throughput virtual screening (HTVS) is not a straight-forward one-size-fits-all process and there are a plethora of issues that need to be addressed before committing yourself to it. We offer multiple levels of support and HTVS protocols, and we encourage you to contact us before choosing an appropriate HTVS package offer.

We highly encourage you to contact us before committing to any of the proposed packages. As we all know, every research project is unique and we will do our best to offer the exact type of analysis and simulations you require. You can leave everything from preparing simulation systems to end-point analysis to us, as well as literature search and guidance of the earliest steps of research. We are committed to providing regular updates, weekly journal clubs, and transparent documentation upon agreement.

Basic HTVS Package

My target is well known, there are multiple PDB structures of it, and I would like to perform screening of a specific and readily available compound library.

If the function of the structure of your target and its ligands are well known, you already have prepared the compound library and want the best insert number here compounds, this is a package for you. Depending on the size and structure of your compound library, HTVS results can be provided up to two weeks after the start of the project.

Extended HTVS Package

My target is well known, there are multiple PDB structures of it, and I would like to perform screening of all commercially available compounds and fragments. Can you also optimize my hits?

This package includes all services available in the Basic HTVS Package. Package for the groups that know their target well and want to perform a full HTVS screening with no prior bias towards a specific pharmacological group of compounds. Custom analysis criteria can be arranged (should it conform to Lipinsky Rule of Five or Three to the letter? If not, how lax can the criteria be? Which ones?) and regular updates via email or video conferences will be organized.

Fragments can then be further optimized and custom synthetic pathways will be suggested.

Full HTVS Package

I know that a certain protein is involved in a process, but I'm not sure how exactly. There are a couple of known fragments of it, could you please model my target? Also, perform a full screening of all available compounds.

This package includes all services available in the Extended HTVS Package. This package is intended for research groups that don't know what is the full structure of their target and functions of it are mostly unknown. Protein can be modeled using DNA code and fragments available in the databases. The model will then further be optimized using molecular dynamics before the HTVS procedure. An extensive literature search is a part of this package, and regular joint research groups journal clubs are encouraged.

Our commitment to Open Source means that every part of our docking workflow done using software developed at RxTx is completely replicable for every research group, provided that you have available hardware and educated team members.

Post-HTVS Processing

We offer advanced molecular dynamics analysis workflows using the GROMACS molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.

Lab Setup

It is a common belief that powerful supercomputers are essential for any kind of "real" research. With the rapid advancement of mainstream hardware, that belief is completely obsolete. Nowadays, all but the most complex simulations that involve millions of atoms on a large time scale can be performed on custom-built PCs that can vary from 1 thousand to 3 thousand euros in cost, depending on your need. Key in building such PCs is in knowing which components are the ones that are important for your type of simulations.

On-site Lab Setup

With our experience in setting up laboratories from scratch, you can leave equipping your in silico laboratory in our hands. We offer consultancy in choosing the right equipment for your lab, as well as providing pre-built PCs and installing the equipment on-site. Moreover, we offer Linux operating systems installation and continued support of software developed in RxTx that is included in docking workflows.

This service is limited to countries within EEA.

Lab in the Cloud Setup

For those who are limited in space or simply prefer having "big iron" elsewhere while planning the workload via a business laptop, we offer setting up a lab in the cloud. We can recommend a provider or work with the provider of your choice (assuming the provider offers a supported hardware and software platform).

This service is offered worldwide.

We encourage you to contact us with specific inquiries.