The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.
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 accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France. Fabio.sterpone@ibpc.fr samuela.pasquali@ibpc.fr Tristan.cragnolini@ibpc.fr maria.kalimeri@ibpc.fr yoann.laurin@ibpc.fr marc.baaden@ibpc.fr phuong.nguyen@ibpc.fr.
Fabio
F
Sterpone
Simone
S
Melchionna
Pierre
P
Tuffery
Samuela
S
Pasquali
Normand
N
Mousseau
Tristan
T
Cragnolini
Yassmine
Y
Chebaro
Jean-Francois
JF
St-Pierre
Maria
M
Kalimeri
Alessandro
A
Barducci
Yoann
Y
Laurin
Alex
A
Tek
Marc
M
Baaden
Phuong Hoang
PH
Nguyen
Philippe
P
Derreumaux
D000682:Amyloid / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
D000682:Amyloid; D011506:Proteins; D012313:RNA; D004247:DNA