Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
Graph Chatbot
Chat with Graph Search
Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.
DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.
A misfolded conformer of the cellular prion protein, denoted as scrapie prion protein, is considered responsible for a variety of fatal neurodegenerative diseases. Both, the function of the protein in its native conformation as well as the factors that tri ...
We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipole ...
The selective and reversible insertion of pseudo-proline (PsiPro) Systems in cyclosporin C (CsC) featuring different C(2) substituents at the oxazolidine ring and its impact on the conformational and biological properties is described. The presence of a 5- ...
Limited searching in the conformational space is one of the major obstacles for investigating protein dynamics by numerical approaches. For this reason, classical all-atom mol. dynamics (MD) simulations of proteins tend to be confined to local energy min., ...
Proteins have a complex free-energy landscape because of their rich topol. and the nature of their nonbonded interaction potential. This has important consequences because the roughness of the landscape affects the ease with which a chain folds and also de ...
Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical sh ...
Intramol. O,N-acyl migration reactions were used as structural switch (S-elements) from a depsipeptide bond contg., unfolded state (Soff) to an all-amide, native states (Son). Chem. or enzymically triggered acyl migrations allowed for the controlled induct ...
Extensive conformational analysis of a series of beta-alkyl substituted cyclopeptides-cyclo(Pro(1)-Xaa(2)-Nle(3)-Ala(4)-Nle(5)-Pro(6) Xaa(7)-Nle(8)-Ala(9)-Nle(10)) and cyclo[Pro(1)-Xaa(2)-Nle(3)-(Cys(4)-Nle(5)-Pro(6)-Xaa(7)-Nle(8)-Cys(9))-N le(10)] as well ...
We present mol. dynamics simulations of bovine rhodopsin in a membrane mimetic environment based on the recently refined x-ray structure of the pigment. The interactions between the protonated Schiff base and the protein moiety are explored both with the c ...
Human retinol-binding protein (RBP) is a monomeric 21-kDa protein that is currently the subject of numerous studies owing to its role in the cellular uptake and utilization of retinol. When the RBP gene is overexpressed in Escherichia coli, inclusion bodie ...