Děkujeme žadatelům za zájem o 1. kolo grantové soutěže pro institucionální a komunitní přístup. V tomto kole byly podány dva projekty, které alokační komise vyhodnotila jako přínosné a podpořila jejich realizaci prostřednictvím cloudových služeb e-INFRA CZ. Alokační komise vyhověla oběma žádostem v plné výši.
The Loschmidt Laboratories Protein Engineering community web-accessible services
Výzkumná organizace: Masarykova univerzita
Řešitel: Joan Planas Iglesias
Traditional protein engineering relies heavily on wet-lab experimentation, a time-consuming and resource-intensive process. The protein engineering tools developed in Loschmidt Laboratories equip researchers in protein engineering, biochemistry, oncology, and related fields with a comprehensive suite of tools for design and analysis of proteins. For protein design, we offer a versatile toolkit to discover new enzymes with desired functions, improve the stability of existing proteins, design ancestral proteins, enhance protein activity, and modify protein specificity. All these properties are targeted through the introduction of specific mutations identified by our predictions. For protein analysis, we provide tools to assess protein solubility, aggregation propensity, detection of tunnels and cavities, ligand binding and unbinding, the impact of mutations in proteins related to oncological diseases, protein denaturation, and melting temperature. Moreover, we develop biological databases to gather datasets for protein stability, solubility, and access pathways in proteins. These databases are an excellent source for training and testing of novel machine learning tools for protein engineering. Our tools are used by more than 100,000 users annually from all around the world.
IDA: Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations
Výzkumná organizace: Univerzita Palackého v Olomouci
Řešitel: Michal Otyepka
Molecular dynamics (MD) simulations are essential for studying nucleic acids (RNA, DNA), proteins, and other biomolecular systems, and they generate huge amounts of data. However, efficient storage, accessibility, and reuse of this data remain significant challenges. To address this, we are developing IDA https://ida.4sims.eu/IDA (Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations [1]), a comprehensive and standardized repository for diverse MD datasets. IDA supports various MD approaches, including standard MD simulations, importance sampling techniques, simulated annealing, and enhanced sampling methods such as replica-exchange simulations. A key feature of IDA is the unique storage and integration of molecule-specific force fields (FFs) alongside MD outputs and experimental datasets, ensuring consistency. By organizing data in a structured format with metadata and persistent identifiers, IDA enables effective data mining and the discovery of valuable insights from the vast data produced by diverse MD simulations. Public accessibility of IDA will eliminate multiple running MD simulations, reducing computational costs and resource consumption while providing a robust foundation for analysis and parameterization. The database will continue evolving with innovative functionalities, expanding its impact on the scientific community and advancing FAIR principles for MD data.