Coarse-grained protein models and their applications
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 …
remains difficult for many protein systems. It is mostly due to the size of protein …
Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies
J Nasica-Labouze, PH Nguyen, F Sterpone… - Chemical …, 2015 - ACS Publications
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 …
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …
The power of coarse graining in biomolecular simulations
HI Ingólfsson, CA Lopez, JJ Uusitalo… - Wiley …, 2014 - Wiley Online Library
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides
P Thevenet, Y Shen, J Maupetit, F Guyon… - Nucleic acids …, 2012 - academic.oup.com
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 …
on-line resource for 3D structure prediction of peptides with well-defined structures in …
PEP-FOLD: an online resource for de novo peptide structure prediction
J Maupetit, P Derreumaux, P Tuffery - Nucleic acids research, 2009 - academic.oup.com
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 …
remain a challenge for chemical biologists. We present PEP-FOLD, an online service, aimed …
A fast method for large‐scale De Novo peptide and miniprotein structure prediction
J Maupetit, P Derreumaux… - Journal of computational …, 2010 - Wiley Online Library
Although peptides have many biological and biomedical implications, an accurate method
predicting their equilibrium structural ensembles from amino acid sequences and suitable …
predicting their equilibrium structural ensembles from amino acid sequences and suitable …
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
F Sterpone, S Melchionna, P Tuffery… - Chemical Society …, 2014 - pubs.rsc.org
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 …
since its first release 15 years ago. The model, which combines energetic and structural …
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ 16–22 dimer and trimer
PH Nguyen, MS Li, P Derreumaux - Physical Chemistry Chemical …, 2011 - pubs.rsc.org
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 …
amyloid peptide assembly. To this end, we performed extensive replica exchange molecular …
Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged …
W Han, K Schulten - Journal of chemical theory and computation, 2012 - ACS Publications
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 …
solvent (J. Chem. Theory Comput. 2010, 6, 3373), has been further optimized, aiming to …
HiRE-RNA: a high resolution coarse-grained energy model for RNA
S Pasquali, P Derreumaux - The journal of physical chemistry B, 2010 - ACS Publications
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 …
structures is increasing and our knowledge of RNA thermodynamics and long time scale …