Preparation of biological macromolecules in the pure state requires that cells be disrupted,
releasing and mixing the contents. Only the most stable and highly structured molecules can …

During the 50 years of NMR, the technology has renewed itself again and again although
the basic physical principles remain the same. As technical advances and novel materials …

We present parmbsc1, a force field for DNA atomistic simulation, which has been
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …

The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …

Advances in molecular dynamics (MD) software alongside enhanced computational power
and hardware have allowed for MD simulations to significantly expand our knowledge of …

Although molecular dynamics (MD) simulations have been used extensively to study the
structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based …

DNA sequence is a major determinant of the binding specificity of transcription factors (TFs)
for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with …

We present a method and web server for predicting DNA structural features in a high-
throughput (HT) manner for massive sequence data. This approach provides the framework …

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al.
AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were …