Advanced in silico small molecule and protein design services via the ProtoDiscovery™ platform

Our Services

We understand that each drug discovery campaign is unique. We provide comprehensive packages of work with a flexible approach and optimised workflows to deliver bespoke solutions that work for clients in the areas of small molecule ligand-based design, structure-based design, virtual screening and enzyme, antibody and other protein engineering.

In addition to the application of bespoke methodologies developed in our group we also provide industry known protocols for example through the use of MOE (Chemical computing group) and Rosetta.

Our group is constantly developing new methods including novel ligand generation approaches using AI and is committed to providing access to the most recent effective methods to our customers.

Services Provided

Small Molecules

 Hit Finding

  • Virtual screening, ligand- and structure-based
  • RxNfinity, ultra large library screening and design
  • Scaffold hopping
  • PPI interactions
  • Metastable protein states
  • Generative AI

Lead optimisation

  • FEP and MMPBSA affinity prediction
  • Molecular dynamics and occupancy studies
  • SAR development via virtual libraries and screening
  • Property optimisation, generative AI MPO problems
  • ADMET and off-target prediction
  • Generative AI


  • Computational design of protein catalysts – higher activity, improved physical properties
  • Design of same function, new sequence space proteins


  • Humanisation
  • Improving physical properties
  • Novel linker design
  • Affinity maturation
  • Cross-species knock-in and knockout

Technology Areas


RxNfinity™ is a dynamic chemical space allowing for virtual screening of billions of compounds against a client’s target.  The screening method incorporates advanced virtual screening capabilities such as customised physics-based scoring and pharmacophores.  The reaction schemes underpinning the approach are carefully selected by our chemists to identify synthetically tractable drug-like molecules.


ProtoScoreRF™  is an empirical scoring function for protein-ligand interaction energies, enabling rapid virtual screening with over 10 million available compounds against diverse targets. Benchmarking studies show superior accuracy compared to industry standard algorithms.

Emperor is a classification technology used alongsideProtoScoreRF™ to identify potential false positives from screening and is trained on known and decoy binding compounds.

Protein Modelling Services


Lead optimisation is affected by the construction of virtual libraries, the use of RxNfinity™, ProtoBuild™, and affinity prediction through ProtoScoreRF™ and FEP.


ProsaRx provide access to a bespoke toolkit for protein design and optimisation, via algorithms such as ASA and ProShuffle™. Our protein engineers are experts in using toolkits such as MOE and Rosetta. Services offered include:
• Protein affinity maturation
• Protein stability prediction
• IP analysis and optimisation strategies


This state-of-the-art screening software includes ProtoScoreRF™, an advanced scoring function benchmarked to be more accurate than other industry standards and a regularly updated compound database (PCD) of >10 million available compounds pre-screened for drug-likeness. An increased coverage of compound conformational space with respect to industry standard protocols is enabled.


  •  Antibody model construction and binding interaction analysis
    • In silico affinity optimisation prediction
  • Assessment of residue changes for humanisation
  • Assessment for developability and potential liabilities

For Antibody Discovery/Galaxy® library, please see our sister company RxBiologics.

rxbiologics logo

Intellectual property

The ProsaRx team have had significant experience in assessing intellectual property and establishing project strategies for FTO for both small molecule and protein designs. Talk to us about your problems – we offer services to assess your field of interest either to provide support for investment potential or for an independent project view within an existing project.

We are a highly experienced computational team of problem solvers. We are flexible in how we work which frequently involves iterative rounds with our clients. We have an extensive track record in identifying and optimising active compounds for both recognised and novel targets as well as in optimising and designing proteins for property improvement (both for SynBio and Pharma objectives). We have a differentiated technology in small molecule design and implement novel approaches to protein design.