GA4GH: International policies and standards for data sharing across genomic research and healthcare
In this perspective, we present the GA4GH strategies for addressing the major challenges of the data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy.
Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells.
MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations
We present here MetaScore, a new machine-learning based approach to improve the scoring of docked conformations. MetaScore utilizes a random forest (RF) classifier trained to distinguish near-native from non-native conformations using a rich set of features extracted from the respective protein-protein interfaces. These include physico-chemical properties, energy terms, interaction propensity-based features, geometric properties, interface topology features, evolutionary conservation and also scores produced by traditional scoring functions (SFs).
Information-Driven Modeling of Biomolecular Complexes
Proteins play crucial roles in every cellular process by interacting [...]
Alchemical absolute protein–ligand binding free energies for drug design
The recent advances in relative protein–ligand binding free energy calculations [...]
