IBERCIVIS - Citizens Donate Personal Computer Time to Science: Projects SOLUVEL and AMILOIDE

Schools may also be involved in the IBERCIVIS (site in Portuguese) platform by providing their computers, thus allowing students and teachers not only contribute to scientific advance, but also to be in touch with the research done at national and foreign laboratories (see Stimulation IBERCIVIS Initiative - Make Your Computer Science Promoting the Initiative IBERCIVIS – Your Computer Doing Science).

The collaboration between Portugal and Spain in this initiative was decided in the cooperation agreements signed at the XXIV Portugal – Spain Summit, on the 22nd of January 2009, in Zamora, Spain, with the objective of extending to Portugal the initiative launched in Spain in 2008, with the support in Portugal, of the Knowledge Society Agency (UMIC), FCCN – Foundation for National Scientific Computing and Ciência Viva – National Agency for the Promotion of Scientific and Technological Culture.

The project SOLUVEL (site in Portuguese) aims to predict the solubility of drugs and toxins, essential to know the adsorption of chemical compounds in living being as they have to pass through cell membranes which involves interaction with hydrophobic and hydrophilic environments. The solubility is directly related to the partition coefficient of the compound between an aqueous phase and an organic phase, which can be estimated from the energy of solvation of the compound in both phases which can be estimated by molecular simulation. This project is of the responsibility of a team of Associate Laboratory LSRE – Laboratory of Separation and Reaction Processes coordinated by Miguel Jorge, of the LSRE and the Faculty of Engineering of University of Porto, who won an IBM Science Prize 2008 Honors Citation at a ceremony held on July 22, 2009, for the paper "Synthesis of Molecular Simulation of Nanoporous Silicas", when the President of the Knowledge Society Agency (UMIC) talked to him about the possibility of preparing a project based on molecular dynamics simulations of the kind presented in the prize session within the IBERCIVIS – Your Computer Does Science initiative.

The project AMILOIDE (site in Portuguese), coordinated by Prof. Rui Brito of the Associate Laboratory CNC – Center of Neurosciences and Cell Biology, aims at computationally searching in libraries of millions of compounds for potential drugs that can interfere with the formation of amyloid aggregates and fibres in neurodegenerative diseases. Its main targets are the Familial Amyloid Polyneuropathy (FAP) and Alzheimer's disease. In about 16 months, the project Amyloid tested computationally in the volunteer computing system IBERCIVIS more than 2.3 million compounds in three target configurations, i.e., nearly 7 million tests, using CPU time of order 8 million hours. It is so far the IBERCIVIS project that used more computational resources. A work that on an ordinary 32-bit personal computer in permanent use would take about 455 years was done in just 16 months on citizens computers available part-time.

The simulations carried out in the project AMILOIDE (site in Portuguese) allowed the identification of several compounds with high potential for possible drugs whose lab tests are already being made. This project is of the responsibility of scientists of the Group of Structural and Computational Biology of the Associate Laboratory CNC – Center of Neurosciences and Cell Biology and the University of Coimbra. A short movie about the project AMILOIDE (site in Portuguese), by Carlos Simões of the CNC, was awarded the SPB/TTW – Connecting Science to People, awarded at the XVII National Congress of Biochemistry, on 15-17 December 2010. The project also let to scientific publications, one of which is already published: Carlos J. V. Simões, Trishna Mukherjee, Rui M. M. Brito, and Richard M. Jackson, Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Method, J. Chem. Inf. Model., 2010, 50 (10), pp 1806-1820.

IBERCIVIS is an Iberian platform, with physical and human resources in Spain and Portugal, which currently supports several scientific projects of research groups in Portugal, Spain, Argentina and Mexico, and soon also from Brazil and Cuba, among which, besides the projects SOLUVEL (site in Portuguese) and AMILOIDE (site in Portuguese) other projects for: analysis of structural properties of amino acids and small peptides (sequences of a few dozen amino acids) that act on the brain and the nervous system (NEUROSIM); adsorption of PILCS (pillared clays) very important for catalysis (e.g., in the production of biofuels from vegetable fats), storage of gases (such as natural gas or gaseous pollutants from the greenhouse effect) and separation processes (ADSORPTION); study of how impurities in materials affect the ability of a quantum wire to conduct electrical current (CUANTICABLES); improvement of the application of ionizing radiation in medicine for diagnosis and treatment of cancer (SANIDAD); study of the effects of systems fractality in the transition metal-insulator when used for electron transport (CRITICALIDAD); simulation of behavior of plasmas that will be produced in the future nuclear fusion reactor ITER – International Thermonuclear Experimental Reactor in Cadarache, France (FUSION); docking of ligands to proteins in seeking drugs for certain types of cancer (DOCKING); simulation of the behavior of magnetic materials with impurities (MATERIALES); simulation of the behavior of light at nanoscale important for building new materials (NANOLUZ); study of the social network underlying IBERCIVIS for analysis of dynamic processes such as synchronization, propagation of viruses or rumors, or models of cooperation-treason (IBERNET). All these projects are described in the Internet portal IBERCIVIS (site in Portuguese) (http://www.ibercivis.pt/).

The Program of the Session on the 1st of July 2011, at the Museum of Science of University of Coimbra, from 14:45 to 16:30, is the following:

• Opening, Paulo Gama Mota, Director of the Museum of Science of University of Coimbra
• e-Science, Luís Magalhães, President of the Knowledge Society Agency (UMIC)
• Volunteer Computing and IBERCIVIS, Rui Brito, IBERCIVIS Coordinator in Portugal, Coimbra University and Associate Laboratory CNC – Centre of Neurosciences and Cell Biology
• IBERCIVIS in Spain and Latin America, Alfonso Tarancon Lafita, IBERCIVIS Coordinator in Spain, University of Zaragoza
• AMILOIDE (site in Portuguese): in search of drugs against neurodegenerative diseases, Carlos Simões, CNC
• SOLUVEL (site in Portuguese): prediction of solubility of drugs and toxins, Miguel Jorge, Faculty of Engineering of University of Porto and Associate Laboratory LSRE – Laboratory of Separation and Reaction Processes
• Demonstration of the registration procedure and of the IBERCIVIS portal, Cândida Silva, CNC.