Protein structure models, biophysical data
and high-performance computing
for drug design

AIC2022 International School


7th September (Day 1)
13.15 -14.15 Registration
14.15 -15.00 We all need models...
Silvia Onesti
15.00-15.45 The role of MX in protein-ligand interaction study
Roberto Steiner
15.45-16.15 Coffee break
16.15-17.00 Kinetics and thermodynamic of protein–ligand binding
Menico Rizzi
17.00-17.45 The role of SAXS and Cryo-EM in protein-ligand interaction study
Federico Forneris
8th September (Day 2)
9.00-10.00 Computational protein model generation: AlphaFold and RoseTTAFold
Anna Marabotti
10.00-11.00 Introduction on structure- and ligand-based drug design
Maria Letizia Barreca
11.00-11.15 Coffee break
11.15-12.15 Protein-inorganic ligand interactions
Adriana Pietropaolo
12.15-13.15 Principles of small molecules docking
Angelo Spinello
13.15-14.15 Lunch
14.14-15.45 PRACTICALS: Practical approach to docking
Giuseppe Felice Mangiatordi
15.45-16.15 Coffee break
16.15-17.00 PRACTICALS: Quality assessment of protein-ligand docking
Giuseppe Felice Mangiatordi
17.00-17.45 Question time
9th September (Day 3)
9.00-10.00 Biophysical studies of protein-ligand adducts
Luigi Scietti
10.00-11.00 Sample preparation and MX data collection for fragment and ligand screening
Manfred Weiss
11.00-11.15 Coffee break
11.15-12.15 Fragment-based drug design
Mattia Sturlese
12.15-13.15 Fitting ligands into MX/CryoEM electron density
Rob Nicholls
13.15-14.15 Lunch
14.14-15.45 PRACTICALS: Coot and phenix tools for ligand finding
Rob Nicholls
15.45-16.15 Coffee break
16.15-17.00 PRACTICALS: Preparing a CIF file for ligand molecules
Belviso Benny Danilo
17.00-17.45 Question time
10th September (Day 4)
9.00-10.00 Role of molecular dynamics in drug discovery
Alessandra Magistrato
10.00-11.00 Innovative small molecule degraders affecting protein folding
Andrea Astolfi
11.00-11.15 Coffee break
11.15-12.15 Advanced MD-based methods for fragment-protein studies: Supervised Molecular Dynamics
Mattia Sturlese
12.15-13.15 TES-1025: a case study for structural validation of protein-ligand interactions
Michele Cianci
13.15-14.15 Discussion and closing remarks
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