EXSCALATE Updates

EXaSCale smArt pLatform Against paThogEns


“There are no incurable diseases — only the lack of will.
 There are no worthless herbs — only the lack of knowledge”
Avicenna (ابن سینا‎) (The Canon Of Medicine) c. 980 – 1037

NEWS

Relevant EXSCALATE News

Antarex calcola con intelligenza i farmaci per bloccare le epidemie V Edizione del FESTIVAL DELLA SCIENZA MEDICA. INTELLIGENZA DELLA SALUTE - VENERDÌ 14 GIUGNO, 10.00 – AULA MAGNA DI SANTA LUCIA. Speaker Marcello Allegretti, Chief Scientific Officer Dompé

VIDEO

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LiGen™ a new Drug Discovery software

Binding Site Analisys

Ultra Fast Geometric Docking

Pharmacophore-driven Docking

Optimized Interaction Pattern

ANTAREX4ZIKA virtual screening simulation.

1.2 Billion small molecular-weight molecules.

PRESS

EXSCALATE Media and communications

PUBLICATIONS

A Collection of Publications about EXSCALATE

LiGen Publications



Ligen
1

Tunable Approximations to Control Time-to-Solution in an HPC Molecular Docking Mini-App

Gadioli D et al. 2019

The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it interacts with the target protein binding site. This task is often done for virtual screening a huge set of molecules to find the most promising ones, which will be forwarded to the later stages of the drug discovery process. Given the huge complexity of the problem, molecular docking cannot be solved by exploring the entire space of the ligand poses. State-of-the-art approaches face the problem by sampling the space of the ligand poses to generate results in a reasonable time budget. In this work, we improve the geometric approach to molecular docking by introducing tunable approximations.

2

LiGen: a high performance workflow for chemistry driven de novo design

Beccari AR et al. 2013

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows

3

Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program

Beato C et al. 2013

On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module LiGenPocket, aimed at the binding site analysis and structure-based pharmacophore definition. We also report the optimization procedure we have carried out to improve the cognate docking and virtual screening performance of LiGenDock. In particular, we applied the design of experiments (DoE) methodology to screen the set of user-adjustable parameters to identify those having the largest influence on the accuracy of the results.

Antarex Publications



1

Autotuning and adaptivity in energy efficient HPC systems: The ANTAREX toolbox.

Designing and optimizing applications for energy-efficient High Performance Computing systems up to the Exascale era is an extremely challenging problem. This paper presents the toolbox developed in the ANTAREX European project for autotuning and adaptivity in energy efficient HPC systems. In particular, the modules of the ANTAREX toolbox are described as well as some preliminary results of the application to two target use cases. 2018 ACM International Conference on Computing Frontiers, CF 2018 - Proceedings, 2018, ACM DOI: 10.1145/3203217.3205338

2

The ANTAREX tool flow for monitoring and autotuning energy efficient HPC systems.

This paper presents the ANTAREX tool flow and shows the impact of optimization strategies in the context of one of the ANTAREX use cases related to personalized drug design. We show how simple strategies, not devised by typical compilers, can substantially speedup the execution and reduce energy consumption. Proceedings - 2017 17th International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2017, 2017, IEEE DOI: 10.1109/SAMOS.2017.8344645

3

AutoTuning and Adaptivity appRoach for Energy efficient eXascale HPC systems: the ANTAREX Approach.

The main goal of the ANTAREX 1 project is to express by a Domain Specific Language (DSL) the application self-adaptivity and to runtime manage and autotune applications for green and heterogeneous High Performance Computing (HPC) systems up to the Exascale level. Key innovations of the project include the introduction of a separation of concerns between self-adaptivity strategies and application functionalities. Design, Automation & Test in Europe Conference & Exhibition, 2016, IEEE DOI: 10.3850/9783981537079_1012

4

The ANTAREX Approach to Autotuning and Adaptivity for Energy Efficient HPC Systems.

The ANTAREX project aims at expressing the application self-adaptivity through a Domain Specific Language (DSL) and to runtime manage and autotune applications for green and heterogeneous High Performance Computing (HPC) systems up to Exascale. The DSL approach allows the definition of energy-efficiency, performance, and adaptivity strategies as well as their enforcement at runtime through application autotuning and resource and power management. Proceedings of the ACM International Conference on Computing Frontiers, 2016, ACM DOI: 10.1145/2903150.2903470

5

ANTAREX - AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems.

The main goal of the ANTAREX project is to express by a Domain Specific Language (DSL) the application self-adaptivity and to runtime manage and autotune applications for green and heterogeneous High Performance Computing (HPC) systems up to the Exascale level. 18th IEEE International Conference on Computational Science and Engineering, 2015, IEEE DOI: 10.1109/CSE.2015.58

EVENTS

Events involving EXSCALATE

Global Biotech Entrepreneurship Excellent opportunity to discuss of the future of pharma at the Taiwan Forum- Innovation Beyond Borders hosted by the Temple University in Philadelphia.

HPC for Industry 4.0@Cineca The aim of the workshop is to present the state-of-the-art of Industry 4.0 technologies in particular, presenting methods and techniques that might be used to transform a manufacturing plant into a plant 4.0. The programme will include the relation among High Performance Computing (HPC), Artificial Intelligence (AI), Big Data and visualization: the basic ingredients to create a digital twin of your 4.0 factory.

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