Search for dissertations about: "All-atom protein models"

Showing result 1 - 5 of 9 swedish dissertations containing the words All-atom protein models.

2. 1. Modelling Biomolecular Interactions of Protein Solutions : Combining Theories and Experiments

   Author : Marco Polimeni; Beräkningskemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular modelling; Protein Solutions; Bio-inorganic Interfaces; Coarse-Grained Models; All-Atom Models; MC simulations; MD simulations; Light Scattering LS ; Small-angle X-ray scattering SAXS ;

   Abstract : Nowadays, interactions of proteins in salt solutions and at the interface with inorganic surfaces are widely investigated as their understanding has numerous applications in medical, pharmaceutical, and biotechnological industries. However, studying these interactions is a complex task that requires appropriate strategies. READ MORE

4. 2. Protein dynamics: aggregation and mechanical unfolding

   Author : Simon Mitternacht; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Monte Carlo simulations; All-atom protein models; Mechanical unfolding; Protein aggregation;

   Abstract : The subject of this thesis is protein dynamics. Papers I--IV and VI study either of two different processes: mechanical unfolding and aggregation. Paper V presents a computationally efficient all-atom model for proteins, variants of which are used to perform Monte Carlo simulations in the other papers. READ MORE

5. 3. Modeling of Protein Folding and Genetic Networks

   Author : Fredrik Sjunnesson; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Matematisk och allmän teoretisk fysik; thermodynamics; two-state folding; Protein folding; all-atom model; Mathematical and general theoretical physics; Kauffman model.; local update; Monte Carlo; classical mechanics; quantum mechanics; relativity; statistical physics; gravitation; klassisk mekanik; kvantmekanik; relativitet; statistisk fysik; termodynamik; Fysicumarkivet A:2003:Sjunnesson;

   Abstract : Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. READ MORE

6. 4. An evolutionary basis for protein design and structure prediction

   Author : Christoffer Norn; Biokemi och Strukturbiologi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Protein evolution; Biophysics; Protein design; Protein structure prediction;

   Abstract : The sequence diversity of protein families is a result of the biophysical selection pressures that shaped their evolutionary history. Among the dominant pressures is selection for protein thermostability, which in itself is an attractive target in protein engineering because of its importance for various biopharmaceutical properties, the performance of industrial enzymes, and the ability to design new protein functions. READ MORE

7. 5. Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins

   Author : Stephanie Jephthah; Beräkningskemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; molecular dynamics; force field; Monte Carlo; coarse-grained modeling; simulation; intrinsically disordered protein; histatin 5; small-angle x-ray scattering; circular dichroism; atomistic MD simulations; all-atom protein models;

   Abstract : The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. READ MORE