Essays about: "protein backbone"

Showing result 1 - 5 of 10 essays containing the words protein backbone.

  1. 1. Design and Evaluation of Peptide Binders : In silico evaluation and comparison of generative AI for de novo peptide binder design

    University essay from Uppsala universitet/Beräkningsbiologi och bioinformatik

    Author : Linde Brokmar; [2023]
    Keywords : Protein design; de novo design; protein engineering; generative ai; machine learning; peptide binders; AF2; EvoBind; RFdiffusion; ProteinMPNN;

    Abstract : Peptide binders are short proteins that bind to larger proteins. Due to peptide binders having high specificity and being cheap to synthesize, they are a prime candidate for drug design. Creating new proteins in silico can be divided into three steps: protein backbone generation, sequence design, and computational filtering. READ MORE

  3. 2. Benchmarking a memetic algorithm for global all-atom protein-protein docking with backbone flexibility

    University essay from Lunds universitet/Kemiska institutionen

    Author : Vera Karlin; [2022]
    Keywords : biochemistry; EvoDOCK; algorithm; protein; iRMSD; DockQ; CAPRI; Chemistry;

    Abstract : Determining how proteins interact with each other to form complexes is very important for understanding both disease and cellular functions, but experimentally determining the structures of these complexes is both tedious and slow, which is why a great number of protein-protein docking algorithms have been developed to predict them. To this day, conformational changes in protein backbones have been one of the largest challenges when making docking predictions. READ MORE

  4. 3. Drug Design of β-Lactamase Inhibitors of the DBO-scaffold against OXA-48 : A Molecular Dynamics Study of Ligand Stability in the Michaelis Complex

    University essay from Uppsala universitet/Läkemedelsdesign och läkemedelsutveckling

    Author : Linda Liljeholm; [2022]
    Keywords : OXA-48; β-lactamase; DBO inhibitors; diazabicyclooctane; avibactam; relebactam; β-lactamase inhibitor; BLI; molecular dynamics; LIE; Linear Interaction Energy; antibiotic resistance; drug design;

    Abstract : The emergence of β-lactamase-mediated antibiotic resistance is one of the biggest threats in modern times. Combined with the discovery void of new forms of antibiotics, this sets the course toward a future where the efficacy of present-day health care will be jeopardized. READ MORE

  5. 4. Assignment of heteronuclear methyl-NMR spectrum of the 44 kDa protein MALT1 Casp-IgL3

    University essay from Lunds universitet/Beräkningsbiologi och biologisk fysik - Genomgår omorganisation

    Author : Maria Levkovets; [2022]
    Keywords : MALT1; NMR; methyl-NMR; protein NMR; Physics and Astronomy;

    Abstract : Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) plays an important role in the immune pathway that controls the activation and proliferation of B and T cells. Dysregularization of this pathway leads to the development of highly aggressive lymphomas. READ MORE

  6. 5. The use of Gibson Assembly for DNA cloning

    University essay from KTH/Tillämpad fysik

    Author : Samuel Johansson; [2022]
    Keywords : Plasmid; Primer; Cloning; PCR; Gibson-Assembly; Transfection; Fluorescent protein; Fluorescent imaging; mCherry; EGFP; Zona-Occludens 1; Occludin; alphaTubulin; Cx-43-7; Plasmid; Primer; Kloning; PCR; Gibson-Assembly; Transfektion; Fluorescerande protein; Fluorescerande avbildning; mCherry; EGFP; Zona-Occludens 1; Occludin; alphaTubulin; Cx-43-7;

    Abstract : This thesis report revolved around the cloning process of plasmids. Attempts of cloning the red fluorescent protein mCherry, and the green fluorescent protein EGFP from various plasmids, into other plasmids containing different cell-junction/cytoskeleton plasmids were made. READ MORE