Search for dissertations about: "Binding affinities prediction"

Showing result 1 - 5 of 6 swedish dissertations containing the words Binding affinities prediction.

  2. 1. Computational Prediction Models for Proteolytic Cleavage and Epitope Identification

    Author : Liwen You; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; medical informatics; biomathematics biometrics; Bioinformatics; SVM; sequence analysis; rule extraction; protease-peptide interaction; OSRE; MHC; immunology; HIV; hierarchical method; HCV; Gaussian process; false positive; epitope; cleavage specificity; cleavage prediction; binding affinity; caspase; Bioinformatik; medicinsk informatik; biomatematik; Computer science; numerical analysis; systems; control; Datalogi; numerisk analys; system; kontroll; Binding affinity; Bioinformatics;

    Abstract : The biological functions of proteins depend on their physical interactions with other molecules, such as proteins and peptides. Therefore, modeling the protein-ligand interactions is important for understanding protein functions in different biological processes. READ MORE

  4. 2. Computational prediction of ligand binding in peptide G-protein coupled receptors

    Author : Silvana Vasile; Hugo Gutiérrez-de-Terán; Johan Åqvist; Herman Van Vlijmen; Uppsala universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; GPCR; neuropeptide Y; angiotensin II receptor; molecular dynamics; free energy perturbation; homology modelling; computer simulations; peptide binding; peptidomimetics; binding free energy.;

    Abstract : G-protein coupled receptors (GPCRs) are a superfamily of membrane receptors involved in a wide variety of biological processes, and their malfunction is associated with many diseases. Consequently, GPCRs are targeted by one-third of the drugs on the market, and constitute the focus of active public and private research in the search of more effective drugs. READ MORE

  5. 3. Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes

    Author : Lars Boukharta; Johan Åqvist; Christopher A. Reynolds; Uppsala universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; computer simulations; molecular dynamics; ligand binding; free energy perturbation; linear interaction energy; binding free energy; homology modelling; structure prediction; alanine scanning; site-directed mutagenesis; hERG; GPCR; neuropeptide Y; HIV-1 reverse transcriptase; integron integrase; Molecular Biotechnology; Molekylär bioteknik;

    Abstract : Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. READ MORE

  6. 4. Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

    Author : Martin Almlöf; Johan Åqvist; Chris Oostenbrink; Uppsala universitet; []
    Keywords : Theoretical chemistry; computer simulations; molecular dynamics; linear interaction energy; binding free energy; linear response; protein-protein interactions; structure-based design; point mutations; hot spots; solvation free energy; Teoretisk kemi;

    Abstract : The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. READ MORE

  7. 5. Computational prediction of receptor-ligand binding affinity in drug discovery

    Author : John Marelius; Uppsala universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Cell and molecular biology; computer-aided ligand design; molecular dynamics simulation; linear interaction energy; free energy perturbation; scoring function; dihydrofolate reductase; thrombin; serine proteases; Cell- och molekylärbiologi; Cell and molecular biology; Cell- och molekylärbiologi; Molecular Biotechnology; molekylär bioteknik avd f jonfysik ;

    Abstract : The evaluation of inhibition constants or, more generally, receptor-ligand binding affinities is a crucial part of the drug discovery process. Chemical synthesis and affinity screening is only affordable for a limited number of compounds. This makes computational methods to predict binding affinities of candidate ligands highly desirable. READ MORE