Institution: IBB
Departement: DSCTM
Typology: Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill, Software
Location: Via Pietro Castellino 111, 80131, Naples
Contacts:
- Luciana Esposito (luciana.esposito@cnr.it)
- Ida Autiero (ida.autiero@cnr.it)
Description:
Background and skills: Recent years have seen ground-breaking achievements of deep-learning methods applied to the 3D structure predictions of biomacromolecules, with the phenomenal success of AlphaFold software in obtaining protein structures at an unprecedented level of accuracy. The availability of huge data on predicted protein structures is revolutionizing the field of experimental structural biology (based on classical X-ray, NMR and Cry-EM methods) making the frontier between experimental and computational approaches more and more blurred. In this context, it is increasingly important to integrate the outcomes from the different techniques in order to favour the mutual exchange, validation, enhancement of experimental and theoretical results. The multiscale computational approach of our team includes both classical and enhanced sampling molecular dynamics (MD) simulations, advanced ab initio quantum-chemical (QM) calculations and computational spectroscopy, protein-protein/ligand-protein/ligand-nucleic acid docking, statistical analysis of structural databases and rational drug design. Facilities: Cluster HP multi CPU: 8 nodes x 2 Intel Xeon Gold 5220R (24-Core); RAID NAS storage (36 TB) Cluster HP multi GPU: 7 NVIDIA A40, 2 x AMD Epyc 64-Core Access to Cineca HPC Systems by approved projects Software: Open source: Gromacs, Amber - MD simulations; Pymol, Chimera, VMD - visualization of molecular structures and trajectories Licensed: Gaussian - QM calculations Ida Autiero, researcher Experience in theoretical modeling, simulations, drug development and algorithm design. Current interest: the characterization of small RNAs at atomistic levels for the rational development of new therapeutics and the understanding of the molecular basis of related cellular processes and diseases. Principal Investigator of PRIN 2022 EpiRNAs. Collaborations: BIDMC Harvard Medical School, USA; Xi'an Jiaotong-Liverpool University, CN. Luciana Esposito, senior researcher Experience in MD simulations, analysis of structural databases, computational modeling of both proteins and DNA/RNA molecules. Current interests: study of the structure and reactivity of DNA/RNA sequences adopting a variety of folds (single strands, duplex, triplex, quadruplex structures), with a special focus to sequences sensible to UV photodamage. Responsible of Cineca IscrC projects. Collaborations: U.A. Madrid, ES. Roberto Improta, research director Consolidated expertise in QM theoretical methods for the study of the ground/excited states of large size biomolecules, particularly in the field of photophysics and photochemistry of nucleic acids. Contribution to methodological advances in computational spectroscopy in solution as well as in the study of photoactivated processes by using quantum dynamical methods. Responsible of task in Spoke6 of CN3 PNRR – Former Coordinator of an ETN ‘Marie Curie’ (LightDyNAmics 2018-2022). Collaborations: DTU Lyngby, DK; CNRS-CEA-U. Strasbourg, FR; U. Brno, CZ; U.A. Madrid-U. Valencia, ES; UCL, UK; U. Ohio-U. California, USA; U. Tel Aviv, IL; East China Normal U., CN. Antonella Paladino, senior researcher Experience in MD, computational physical-chemistry and bioinformatics approaches with a strong focus on studying the dynamics and specificity of biomolecular interactions. Current interest: atomistic characterization of molecular recognition and protein-RNA assemblies, to study the role of conformational dynamics in allosteric regulation for rational drug design. Unit coordinator of PRIN 2022 IONHOF; Collaboration: U. Miami, USA; USI, CH. Luigi Vitagliano, research director Long experience in integrated structural biology. Computational techniques for the definition of the structural and dynamics properties of supramolecular assemblies and complexes. Coordinator of IBB activities of the CN1 PNRR (High Performance Computing). Collaborations: Harvard U., USA; TU Dortmund U., DE. Industrial collaboration: Synlab SDN, IT.
Team:
- Ida Autiero ida.autiero@cnr.it
- Luciana Esposito luciana.esposito@cnr.it
- Roberto Improta roberto.improta@cnr.it
- Antonella Paladino antonella.paladino@cnr.it
- Luigi Vitagliano luigi.vitagliano@cnr.it
- Jorge Franco jorge.franco@ibb.cnr.it (Postdoc, supervisor: A.P.)
- Parnia Jabbari parnia.jabbari@ibb.cnr.it (Postgraduate, supervisor: A.P.)
- Malay Ranjan Biswal malayrjn@gmail.com (Postdoc, supervisor: I.A.)