Search for dissertations about: "molecular mechanics MM"

Showing result 1 - 5 of 20 swedish dissertations containing the words molecular mechanics MM.

  1. 1. A multivariate approach to characterization of drug-like molecules, proteins and the interactions between them

    University dissertation from Umeå : Kemi

    Author : Anton Lindström; Anna Linusson; Fredrik Almqvist; Anders Karlén; [2008]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; binding affinity; prediction; CAMD; principal component analysis PCA ; partial least squares projections to latent structures PLS ; MM-GB-SA; MM-PB-SA; docking; geometry optimization; protein secondary structure characterization; implicit solvent; generalized-Born; Poisson-Boltzmann; molecular mechanics MM ; drug discovery; bindningsaffinitet; prediktion; dockning; geometrioptimering; sekundärstruktur; matematisk vattenmodel; generalized-Born; Poisson-Boltzmann; molekylmekanik MM ; läkemedelsdesign; principal komponent analys PCA ; partial least squares projections to latent structures PLS ; MM-GB-SA; MM-PB-SA; NATURAL SCIENCES Chemistry Other chemistry; NATURVETENSKAP Kemi Övrig kemi;

    Abstract : En sjukdom kan många gånger härledas till en kaskadereaktion mellan proteiner, co-faktorer och substrat. Denna kaskadreaktion blir många gånger målet för att behandla sjukdomen med läkemedel. För att designa nya läkemedelsmoleyler används vanligen datorbaserade verktyg. READ MORE

  2. 2. QM/MM free-energy perturbation and other methods to estimate ligand-binding affinities

    University dissertation from Lund University, Faculty of Science, Department of Chemistry, Division of Theoretical Chemistry

    Author : Martin Olsson; [2018-02]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Computer-aided drug design; protein–ligand binding; molecular dynamics; free-energy perturbation; QM MM; convergence;

    Abstract : Experimental drug discovery is very time-consuming, risky and comes at a huge cost, typically several billion USD per drug. Even though decades of experimental drug discovery have provided cures of many diseases, there are still diseases for which there is no effective drug available. READ MORE

  3. 3. Theoretical studies of porphyrin proteins

    University dissertation from Emma Sigfridsson, Department of theoretical Chemistry, Chemical Centre

    Author : Emma Sigfridsson; [2001]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; molecular mechanics; quantum chemical calculations; electrostatic potential charges; atomic charges; ferrochelatase; cytochrome; myoglobin; Porphyrin; haem; QM MM; reorganisation energy; Theoretical chemistry; quantum chemistry; Teoretisk kemi; kvantkemi;

    Abstract : Different aspects of porphyrin proteins have been studied with theoretical methods. For example, we have studied: - The importance of hydrogen bonds for the discrimination between carbon monoxide and molecular oxygen by myoglobin, the oxygen carrier in muscles, modelling the active site both in vacuum and in the protein matrix - The inner-sphere reorganisation energy during electron transfer for cytochromes compared to other electron-transfer proteins, such as blue copper proteins and Fe-S clusters - The role of porphyrin distortions in the reaction mechanism of ferrochelatase, the enzyme that inserts an iron ion into protoporphyrin IX to make haem - The interaction between different metal sites in ferrochelatase In these studies we have used density functional theory, classical force field methods, and a combination of quantum chemistry and molecular mechanics. READ MORE

  4. 4. Assessment of Computational Methods for Ligand Binding

    University dissertation from Division of Theoretical Chemistry, Department of Chemistry, Lund University

    Author : Paulius Mikulskis; [2015]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; binding affinities; MM GBSA; MM PBSA; LIE; FEP; TI; BAR; protein-ligand complexes; drug design;

    Abstract : Most drugs act on biomacromolecules. The Cost of developing new drugs is very high. A method to accurately predict binding affinities would be very useful. READ MORE

  5. 5. On the estimation of ligand binding affinities

    University dissertation from Department of Chemistry, Lund University

    Author : Samuel Genheden; [2012]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; binding affinities protein-ligand complexes; host-guest complexes; MM GBSA; MM PBSA; LIE; PDLD s-LRA; alchemical methods; sampling; solvation; drug design;

    Abstract : A method to accurately estimate the binding affinity of a small molecule to a receptor would be indispensable in numerous fields. For instance, most drugs exert their action by binding to a macromolecule target. Thus, a lot of time and resources could be saved in drug design by predicting affinities by computer programs. READ MORE