Tools generated in MDAKM
We created an information system to provide access to an organized data set of all genetic replacement mutations that can be found in the NOTCH3 protein, arranged in a database that facilitates their study.
The main goal is understanding the CADASIL syndrome at the genetic level, since mutations in the NOTCH3 protein have been linked with the syndrome, so as to discover useful information that could be applied in the development of pharmaceutical solutions directed against it.
Drugster is a de novo Drug Design platform, which through the versatility of the elite software that it incorporates can efficiently exploit single or multiple processor workstations and achieve high performance through novel and faster custom-made routines. Drugster is a freeware platform aimed to assist scientists in the field of Computer Aided Drug Design (CADD). It facilitates the use of other freeware applications (PDB2PQR, Gromacs, Ligbuilder, Dock) in order to create a pipeline for producing high quality results.
Vlachakis D, Tsagkrasoulis D, Megalooikonomou V, Kossida S. (2012) Introducing Drugster: a comprehensive drug design, lead and structure optimization toolkit. Bioinformatics, 2013, 29(1):126-128. [doi: 10.1093/bioinformatics/bts637]
During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands.
Vlachakis D, Fakourelis P, Megalooikonomou V, Makris C, Kossida S. (2015) DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit. PeerJ, 2015; 13;3:e725. . [doi: 10.7717/peerj.725]