Coarse graining of biomolecules
and beyond

7 October 2017
  Warsaw, Poland

Venue & Travel

  Saturday, Oct 7    
  08:00 - 08:30 registration & morning coffee
Session I
  08:30 - 09:00Piotr Setny (T)
Discrete solvent based method for the prediction of protein hydration sties
  09:00 - 09:30Garegin Papoian (T)
AWSEM-MD: Overview of the Force Field and Selected Applications
  09:30 - 10:30Filip Leonarski (HS)
RedMDStream: Simulation Toolbox To Automatically Parameterize Coarse-grained Force Fields
  10:30 - 11:00 cofee break
Session II
  11:00 - 11:30 Szymon Niewieczerzał (T)
New implicit environment model for the study of membrane proteins manipulations by coarse-grained molecular dynamics
  11:30 - 12:00Adolfo Poma (T)
GoMartini: Study of Large Conformational Transition in Proteins with the Martini Force-Field
  12:00 - 13:00Mateusz Kurcinski, Maciej Ciemny, Tymoteusz Oleniecki, Karolina Dawid, Sebastian Kmiecik (HS)
Modeling of protein flexibility and protein-peptide interactions using CABS-flex and CABS-dock standalone applications
  13:00 - 14:00 lunch
Session III
  14:00 - 14:30Mateusz Sikora (T)
Membrane Glycoproteins in MARTINI Forcefield – a Sticky Problem
  14:30 - 15:00Rafał Jakubowski (T)
Unfolding of membrane proteins with complex topology
  15:00 - 16:00Cezary Czaplewski, Paweł Krupa, Adam Sieradzan (HS)
UNRES, NARES, and SUGRES Coarse-Grained Models - An Introduction
  16:00 - 17:00 poster session & coffee
Session IV
  17:00 - 17:30Michał Boniecki (T)
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
  17:30 - 18:00Filip Stefaniak (T)
Modeling of ribonucleic acid-ligand interactions
  18:00 - 19:00Mateusz Dobrychłop (HS)
PyRy3D: a software tool for modelling of large macromolecular complexes
  19:00 - :) evening get-together

T - talk
HS - hands on session