Software

Drugster Suite

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.

Link: http://www.bioacademy.gr/bioinformatics/drugster/
Citation: 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]


DrugOn Suite

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.

Link: http://www.bioacademy.gr/bioinformatics/drugon/
Citation: 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]


Xplatform Suite

With the extensive use of microarray technology as a potential prognostic and diagnostic tool, the comparison and reproducibility of results obtained from the use of different platforms is of interest. The integration of those datasets can yield more informative results corresponding to numerous datasets and microarray platforms. We developed a novel integration technique for microarray gene-expression data derived by different studies for the purpose of a two-way Bayesian partition modelling which estimates co-expression profiles under subsets of genes and between biological samples or experimental conditions. The suggested methodology transforms disparate gene-expression data on a common probability scale to obtain inter-study-validated gene signatures. We evaluated the performance of our model using artificial data. Finally, we applied our model to six publicly available cancer gene-expression datasets and compared our results with well-known integrative microarray data methods. Our study shows that the suggested framework can relieve the limited sample size problem while reporting high accuracies by integrating multi-experiment data.

Link: http://rsta.royalsocietypublishing.org/content/372/2016/20130136
Citation: Tsiliki G, Vlachakis D, Kossida S. (2014) On integrating multi-experiment microarray data. Phil. Trans. R. Soc. A 2014 372 20130136[doi:10.1098/rsta.2013.0136]


Space Suite

Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.

Link: https://www.hindawi.com/journals/cmmm/2013/108910/
Citation: Vlachakis D, Kontopoulos DG, Kossida S. (2013) Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus. Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 108910, 9 pages. [doi: 10.1155/2013/108910]


Structuprint Suite

BACKGROUND: The term 'molecular cartography' encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors.
RESULTS: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible.
CONCLUSIONS: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists.

Link: https://www.ncbi.nlm.nih.gov/pubmed/26911476/
Citation: Vlachakis D, Tsagkrasoulis D, Megalooikonomou V, Kossida S. (2016) Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Struct Biol. 2016;16:4. [doi: 10.1186/s12900-016-0055-7]