Sökning: "Metadynamics"

Hittade 3 uppsatser innehållade ordet Metadynamics.

1. 1. Aromatic Ring Flips and Local Volume Fluctuations in BPTI

   Master-uppsats, Lunds universitet/Biofysikalisk kemi

   Författare :Simon Enbom; [2022]
   Nyckelord :Biophysical Chemistry; Molecular Dynamics; Protein Dynamics; Activation Volume; Aromatic Ring Flips; BPTI; Biology and Life Sciences; Chemistry; Technology and Engineering;

   Sammanfattning : Aromatic ring flips are a classic example of a dynamic process in proteins. Discovered decades ago, methodological limitations hindered progress at the time. Ring flips have gained new interest and experimentalists can measure the flip rate and thermodynamic quantities associated with it. LÄS MER

3. 2. Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

   Master-uppsats, Lunds universitet/Biofysikalisk kemi

   Författare :Emil Åberg; [2017]
   Nyckelord :GAFF; FXR; farnesoid X receptor; MD; computational; enhanced sampling; binding; receptor; ligand; Simulations; Reconnaissance; Metadynamics; Docking; Molecular Dynamics; Protein; AMBER; force fields; structure prediction; crystallography; collective variables; potential; bias potential; biophysical chemistry; biofysikalisk kemi; Chemistry; Technology and Engineering; Biology and Life Sciences;

   Sammanfattning : A computational method is described and tested for prediction of ligand-binding poses between the human farnesoid X receptor and a set of 36 potential agonists, provided by the D3R Grand Challenge 2016. Using tools such as Molecular Docking, Molecular Dynamics, Reconnaissance metadynamics and cluster analysis, the method is an attempt to predict the binding pose without being biased by experimental data. LÄS MER

4. 3. SAXS-Guided Metadynamics

   Master-uppsats, KTH/Teoretisk fysik

   Författare :Farhad Kimanos; [2014]
   Nyckelord :;

   Sammanfattning : .... LÄS MER