RF-2024-12377665-Postdoctoral Position for a Computational Structural Biologist

Gruppo San Donato; Lombardia; In loco; EUR 29.000 - 30.000; Tempo pieno

Descrizione del lavoro

IRCCS San Raffaele Scientific Institute in Milan, Italy, invites a computational structural biologist to join the Biomolecular NMR Unit. The role centers on MD simulations, AI-driven and physics-based drug discovery, and integration of experimental data to model large biomolecular complexes.

The candidate should have a PhD in Chemical Sciences, strong MD, IMS, and SBDD experience, plus coding and HPC skills. Co.co.co contract; €29,000–€30,000 yearly; based in Milan.

Competenze

• PhD in Chemical Sciences required.
• Expertise in MD simulations, enhanced sampling, CpHMD, MSMs, and free energy calculations.
• Experience with Schrödinger Suite for docking, HTVS, pharmacophore modeling.
• Experience with HADDOCK3 for biomolecular docking and NMR data integration.
• Gaussian parameterization for metal-containing systems.
• Familiarity with AI-based structure prediction methods (AlphaFold, RoseTTAFold, etc.).
• Programming and visualization skills in Bash, Python, PyMOL, and VMD.
• Access to HPC resources and ability to obtain computational grants.

Mansioni

• Virtual screening of small molecules using AI and physics-based methods.
• Molecular docking and diffusion-based modeling for complexes.
• Molecular dynamics to study structure and interactions.
• Protein structure prediction and SBDD tasks.
• Integrate experimental data (cryo-EM, X-ray, NMR) for large complexes.
• Analyze interaction datasets and simulation outputs.
• Maintain Linux workstations, install and update software.

Conoscenze

MD simulations

Enhanced sampling

CpHMD

MSMs

Free energy calculations

Programming (Bash & Python)

Molecular visualization (PyMOL, VMD)

AI-based approaches in structure

HPC usage for large-scale simulations

Linux workstation administration

Grant/wunding HPC access experience

Formazione

PhD in Chemical Sciences

Strumenti

Schrödinger Suite

HADDOCK3

Gaussian

AlphaFold

RoseTTAFold

BindCraft

Chai-1

Boltz

BioEmu

PyMOL

VMD

Linux/UNIX

Descrizione del lavoro

IRCCS San Raffaele Scientific Institute in Milan, Italy, is looking for a computational structural biologist to join the Biomolecular NMR Unit.

Project Code: RF-2024-12377665

Project Title: Drug-like molecules targeting DUX4 in FSHD muscular dystrophy

CUP code: C43C26000440001

Main responsibilities

• Virtual screening of small molecules using both artificial intelligence-based and physics-based methods.
• Molecular docking, including diffusion-based generative models for the prediction of molecular complexes.
• Molecular dynamics (MD) simulations to investigate molecular structure, stability, and interactions.
• Protein structure prediction and modeling.
• Structure-Based Drug Design (SBDD).
• Integration of experimental data (cryo-EM, X-ray crystallography, and NMR) for the reconstruction of large macromolecular complexes.
• Analysis of biomolecular interactions and simulation-derived data.
• Maintenance of Linux workstations, including software installation, configuration, and updates.

The candidate we are looking for has the following skills

• PhD in Chemical Sciences;
• Expertise in molecular dynamics (MD) simulations, enhanced sampling techniques, constant-pH molecular dynamics (CpHMD), Markov State Models (MSMs), and free energy calculations;
• Experience with computer-aided drug discovery and design software (Schrodinger Suite), including molecular docking, high-throughput virtual screening (HTVS), pharmacophore modeling, and binding site prediction;
• Experience with HADDOCK3 (local installation) for biomolecular docking and the integration of experimental NMR data into structural modeling;
• Expertise in metal center parameterization using Gaussian, including quantum mechanical calculations for the development of force field parameters for metal-containing biomolecular systems;
• Experience with artificial intelligence-based approaches for example: AlphaFold, RoseTTAFold, BindCraft, Chai-1, Boltz, BioEmu;
• Proficiency in programming and molecular visualization tools, including independent development of Bash and Python scripts without AI assistance, and molecular visualization using PyMOL and VMD;
• Experience utilizing high-performance computing (HPC) resources for large-scale molecular simulations and computational studies;
• Recipient of computational research grants providing access to HPC infrastructure and computational resources.

What we offer

• Type of contract: co.co.co;
• Gross Annual Fee: € 29.000 - € 30.000;
• Duration: from 15/01/2027 to 31/10/2029;
• Place of work: IRCCS San Raffaele Hospital, Via Olgettina, number 60 - Milan (Italy).

At San Raffaele Scientific Institute, a world-renowned center of excellence for clinical and scientific activities, we believe that considering diversity and promoting an open and inclusive environment is crucial to our success. We are committed to ensure that equal employment opportunities are provided and based on merit without regard to age, religion, sex, disability, medical condition, sexual orientation, cultural and social backgrounds, gender identity or expression, national or ethnic origin, or any other legally recognized status entitled to protection under applicable laws. We offer attractive conditions and rewards appropriate to an internationally competitive research organization