The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …

Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

In the context of the renewed interest of peptides as therapeutics, it is important to have an
on-line resource for 3D structure prediction of peptides with well-defined structures in …

Rational peptide design and large-scale prediction of peptide structure from sequence
remain a challenge for chemical biologists. We present PEP-FOLD, an online service, aimed …

Although peptides have many biological and biomedical implications, an accurate method
predicting their equilibrium structural ensembles from amino acid sequences and suitable …

The OPEP coarse-grained protein model has been applied to a wide range of applications
since its first release 15 years ago. The model, which combines energetic and structural …

The aim of this work is to investigate the effects of molecular mechanics force fields on
amyloid peptide assembly. To this end, we performed extensive replica exchange molecular …

PACE, a hybrid force field that couples united-atom protein models with coarse-grained (CG)
solvent (J. Chem. Theory Comput. 2010, 6, 3373), has been further optimized, aiming to …

Although RNAs play many cellular functions, the gap between their sequences and 3D
structures is increasing and our knowledge of RNA thermodynamics and long time scale …