Your partner in computational drug design
Silicos-it is a Belgian consultancy company, founded in 2010 and specialised in computational drug design. We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models. In addition, we are also involved in writing open source software tools.
Since 2013, a strong relation with the University of Antwerp (UA) was established. Because of this, we can provide you with a complete set of solutions to all your questions related to computational drug design. This may include service work under the wings of the UA, submission and execution of a VLAIO project with the UA as academic partner, or some well-defined fee-for-service projects with Silicos-it as the commercial partner.
Do you like to find out more of what we can do for you? Then have a look at the research examples page on this website for ideas and opportunities. And the who are we page gives you insight into our history and where we are right now.
Do you think we can help you? We are open to many forms of collaboration. Therefore, do not hesitate to contact us to discuss your potential research ideas. Maybe it is the beginning of a mind-blowing research collaboration!
Our latest post
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)
Cosolvent molecular dynamics simulations are molecular dynamics simulations used to identify preferable locations of small organic fragments on a protein target. Most cosolvent molecular dynamics workflows make use of only water-soluble fragments, as hydrophobic fragments would cause lipophilic aggregation. To date the two approaches that allow usage of hydrophobic cosolvent molecules are to use a low concentration of hydrophobic probes, with the disadvantage of a lower sampling speed, or to use force field modifications, with the disadvantage of a difficult and inflexible setup procedure. In this new paper we present a new alternative, that does not suffer from low sampling speed nor from cumbersome preparation procedures. We have built an easy-to-use open source command line tool PART (Plumed Automatic Restraining Tool) to generate a PLUMED file handling all intermolecular restraints to prevent lipophilic aggregation. We have compared restrained and unrestrained cosolvent MD simulations, showing that restraints are necessary to prevent lipophilic aggregation at hydrophobic probe concentrations of 0.5 M. Furthermore, we benchmarked PART generated restraints on a test set of four proteins (Factor-Xa, HIV protease, P38 MAP kinase and RNase A), showing that cosolvent MD with PART generated restraints qualitatively reproduces binding features of cocrystallised ligands.