ABC Meeting 2014

Barcelona,  14th February 2014







Start End Speaker Description
09:00 09:15 Modesto Orozco Welcome
09:15 09:50 Charlie Laughton The ABC3 Dataset: A Cartesian Coordinate Perspective
I will present some preliminary results from our PCA-based investigations of the latest ABC dataset, focussing particularly on multi modality and patterns of dynamical similarity and difference between tetrads.
09:50 10:25 Marco Pasi muABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects on the conformations and fluctuations of B-DNA
I will be discussing the results of the analysis of the recently assembled microsecond-scale dataset of ABC simulations.
10:25 10:45 Coffee break  
10:45 11:20 Richard Lavery Ion distributions around DNA.
11:20 11:55 Jiri Sponer Pair-additive nucleic force fields and their limitations.
I will briefly comment on our recent experience with testing nucleic acids force fields, including simulation studies and lot of benchmark QM calculations. I will explain why, although improvements are possible, we rather assume that we cannot get a perfect nucleic acids force field within the non-polarizable force field approximation.
11:55 12:30 Filip Lankas Performance of the bsc0 force field with ezOL modification in simulations of B-DNA.
12:30 12:50 Ivan Ivani Parmbsc1: a refinement of parmbsc0 for DNA simulations.
12:50 14:50 Lunch informal discussion on ABC roadmap
14:50 15:25 John Maddocks cgDNA: A sequence-dependent coarse-grain ridig base model of B-form DNA parameterised from the ABC database.
15:25 16:00 Sarah Anne Harris

Multiscale modelling of complex DNA topologies: I will describe atomistic MD simulations of closed circular DNA minicircles subjected to superhelical stress. Supercoiling causes the DNA to writhe and denature, and can therefore result complex DNA topologies that are implicated in gene regulation. However, given the large persistence length of DNA, obtaining sufficient statistics to quantify sequence dependent behaviour is challenging. Therefore, we are using a multiscale approach involving coarse-grained simulations and statistical mechanics to assess how bending and superhelical stress give rise to DNA denaturation.

16:20 16:40 Guillem Portella MD and NMR Analyses of Choline and TMA Binding to Du-plex DNA: Origins of Aberrant Sequence-Dependent Stabil-ity by Alkyl Cations in Aqueous and Water-Free Solvents.
16:40 17:00 Giulia Rossetti DNA mismatches
DNA mismatch (MM) is a DNA defect occurring when non-complementary bases are incorporated into DNA helix due to replication errors, heteroduplex formation, mutagenic chemicals and ionizing radiation or spontaneous deamination. Failure of MMs correction by mismatch repair proteins (MMR), or misdirected repair to the strand containing the original and correct DNA sequence, will inevitably give rise to genetic mutations. In this respect, MMs are associated with 10–30% spontaneous cancers in various tissues and hereditary colorectal cancer (Lynch syndrome).
Intriguingly the local stability and geometrical features of MM-containing DNA are roughly correlated with the observed MM repair efficiencies. Thus they may somehow also affect the efficiency of MMR system.
Despite the suggested correlations, up to now there is not a clear picture for how exactly the MMs affect structure and energetic of DNA and how, in turn, these MM-dependent perturbations affect the MMR’s repair efficiency. We investigate these issue by means of computational methods. Specifically we model all the possible MM in three different sequences with different plasticity features.
17:00 17:20 Coffee break  
17:20 17:40 R.Goni, A.Hospital, M.Orozco Data Problems and solutions in ABC
17:40 18:40 R.Lavery coordinator Round table: Next steps 


Please fill the registration form below indicating if you wish to give a talk:



Sala de Juntes del Rectorat, in campus UPC campus nord
Jordi Girona 31, 08034 Barcelona




Our suggestion for a hotel nearby the meeting (10 minutes walking) is:
Hotel HUSA Arenas

If you prefer a hotel closer to the city center (30 minutes with
metro), then we would suggest:
Hotel Catalonia Ramblas



Margarita Pedro

+34 934037155