Sökning: "conformational sampling"

Visar resultat 1 - 5 av 19 avhandlingar innehållade orden conformational sampling.

  1. 1. Sampling from molecular unnormalized distributions with Deep Generative Models

    Författare :Juan Viguera Diez; Chalmers tekniska högskola; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; machine learning; Cheminformatics; conformational sampling; generative models; drug discovery; Boltzmann generators;

    Sammanfattning : This thesis investigates how Deep Generative Models (DGMs) can address important drug discovery problems involving sampling from unnormalized distributions. It consists of two papers focusing on this challenge’s aspects: molecular design and conformational sampling. LÄS MER

  3. 2. Modeling and simulation of intrinsically disordered proteins

    Författare :Joao Henriques; Beräkningskemi; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Intrinsically disordered proteins; Coarse-grained models; Atomistic models; Metropolis Monte Carlo simulations; Molecular dynamics simulations; Sampling; Conformational analysis; Charge regulation; Surface adsorption;

    Sammanfattning : This work is primarily about the development, validation and application of computer simulation models for intrinsically disordered proteins, both in solution and in the presence of uniformly charged, ideal surfaces. The models in question are either coarse-grained or atomistic in nature, and their applications are dependent on the specific purpose of each study. LÄS MER

  4. 3. Computational Modeling of Macrocycles and Structure-Based Design of Novel Antibacterial Compounds

    Författare :Gustav Olanders; Anders Karlén; Peter Brandt; Christian Sköld; Dan Sindhikara; Uppsala universitet; []
    Nyckelord :MEDICIN OCH HÄLSOVETENSKAP; MEDICAL AND HEALTH SCIENCES; macrocycles; docking; conformational sampling; conformational prefer-ences; antibiotics;

    Sammanfattning : The integration of computational methods into the drug discovery process provides valuable tools to help advance new and improved drugs into the clinic. As medicinal chemists explore novel targets and new areas of chemical space, our computational toolkit must also evolve. LÄS MER

  5. 4. New approaches to data-driven analysis and enhanced sampling simulations of G protein-coupled receptors

    Författare :Oliver Fleetwood; Lucie Delemotte; Erik Lindahl; Ulrich Zachariae; KTH; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; GPCR; G protein-coupled receptors; Molecular Dynamics; MD; Enhanced Sampling; beta2 adrenergic receptor; beta2; Biological Physics; Biologisk fysik;

    Sammanfattning : Proteins are large biomolecules that carry out specific functions within living organisms. Understanding how proteins function is a massive scientific challenge with a wide area of applications. In particular, by controlling protein function we may develop therapies for many diseases. LÄS MER

  7. 5. Molecular Recognition and Conformational Dynamics in Macromolecules

    Författare :Soumendranath Bhakat; Biofysikalisk kemi; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Protein; ligand; host-guet; funnel metadynamics; MM PBSA; well-tempered metadynamics; collective variable; tyrosine; aspartic protease; local fluctuations; hydrogen exchange; time-lagged independent component analysis; principal component analysis; parallel-tempering;

    Sammanfattning : Computational methods gained a widespread use in drug discovery. Understanding conformational dynamics of protein and mechanisms of protein-ligand binding are two major areas in drug discovery. Molecular dynamics (MD) simulation have been routinely used to study conformational dynamics of protein and mechanisms of protein-ligand binding. LÄS MER