Funnel metadynamics as accurate binding free-energy method
نویسندگان
چکیده
منابع مشابه
Funnel metadynamics as accurate binding free-energy method.
A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficien...
متن کاملCalculation of free energy landscapes: A histogram reweighted metadynamics approach
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history-dependent bias potential, which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Because of the presence of the bias potential, it can be also used to accelerate rare events. In addition, the calculated fr...
متن کاملLigand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.
G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate th...
متن کاملTowards accurate free energy calculations in ligand protein-binding studies.
Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties o...
متن کاملWell-tempered metadynamics: a smoothly converging and tunable free-energy method.
We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2013
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.1303186110