October 7, 2017


Drug design


Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of the workflow in drug discovery

What’s new

Flocking offers unprecedented ability to design novel protein inhibitors, exploiting all atoms molecular dynamics. It permits to design or optimize small molecules as well as peptides for protein interaction. Flocking is under the patenting process


Generally, when the binding site of a protein is known and a molecule is similar to known ligands, traditional docking methods are rather accurate in the prediction of the interaction. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are usually not accurate.

What’s new

Yada is a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux.
Piotto, S., Di Biasi, L., Fino, R., Parisi, R., & Sessa, L. (2016). Yada: a novel tool for molecular docking calculations. Journal of computer-aided molecular design, 30(9), 753-759.


Biologists and chemists are facing problems of high computational complexity that require the use of several computers organized in clusters or in specialized grids. Regrettably, the diffusion of Grid Computing is strongly limited because two main limitations: it is confined to scientists with a strong Computer Science background and the analyses of a large amount of data produced can be cumbersome it.

What’s new

GRIMD is very flexible because it shields the typical computational biologist from the need to write specific code for tasks such as molecular dynamics or
docking calculations. Furthermore, it permits efficient use of GPU cards whenever is possible. GRIMD calculations scale almost linearly and, therefore,
permits to exploit efficiently each machine in the network.


It is a new concept video game that extends the capabilities of a computer to solve pharmaceutical problems by exploiting human abilities to solve problems heuristically.

What’s new

LandMeIn is the ludic transposition of Yada. The video game is a mix of Treasure Island and Tetris. LandMeIn extends the computer abilities in drug design adding the unsurpassed human mind ability to find patterns. It permits to players to do real drug research. It offers to Big Pharma a brand new way to advertise products.

Computational toxicology


Toxicity prediction suite of a wide array of molecules. More info on www.etox.unisa.it

What’s new

eTox is an in silico tool for predicting ADME properties and the toxic potential (endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity) of small molecules (<500 Dalton). The toxicity potential is evaluated via a fully flexible docking (flexible receptor/flexible ligand) protocol. Currently, eTox permits the investigation of 19 proteins known to trigger adverse effects.

Data Mining


ProtComp is a sequence analysis tool for general purposes. It exploits compression algorithms to build up dictionaries of substrings. These dictionaries are compared by means of ad hoc metrics

What’s new

ProtComp is an algorithm that exploits data compression to perform an alignment-free analysis of textual data. Originally written to perform genomic and proteome analysis and to design new antimicrobial peptides, the algorithm is powerful, flexible, scalable, and applicable in different contexts. ProtComp permits to perform genomic and big data analysis in a tiny fraction of the normal time


A new generation search engine. SM_search is not a Google-like engine. It is an alternative to the traditional search. It is the ProtComp algorithm applied to file search.

What’s new

We are all used to keyword searches. Windows, Androids, Linux, Google, Yahoo, Bing…. all of them do permit to search efficiently among an enormous amount of data. Nevertheless, when you don’t know how to write a query when you don’t remember some significant words, the search process quickly becomes a nightmare. SM_search is a different way to perform a search. Rather than using keywords or tags, consider the whole content of a file to find “similar” objects.


eHealth is a relatively recent healthcare practice supported by electronic processes and communication. Healthcare IT platforms collect data from different devices and sources to provide holistic and real-time information on patients. Today, new IT platforms are starting to appear that can deliver a variety of services to the provider faster.

What’s new

SM_health is an application of the ProtComp algorithm to automatically detect similarity in EEG and ECG. The process is in real-time and takes place on the device. The main difference with existing software is that instead of searching for a pattern in an ExG, it analyses the whole dataset in real time. No privacy problem, no cloud-based app, no connection problem.


In computing, a file system is used to control how data is stored and retrieved. Semantic file systems are file systems used for information persistence which structure the data according to their semantics and intent, rather than the location as with current file systems. Semantic file systems raise technical design challenges as indexes of words, tags or elementary signs of some sort have to be created and constantly updated, maintained and cached for performance

What’s new

Semantic_FS is an application of the ProtComp algorithm to create a dynamic file system on your computer or smartphone. It organizes the files on the basis of their similarity. It complements the SM_search and permits to reorganize your data efficiently and rationally.