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  2. Path integral molecular dynamics - Wikipedia

    en.wikipedia.org/wiki/Path_integral_molecular...

    The simulations done my PIMD can broadly characterize the biomolecular systems, covering the entire structure and organization of the membrane, including the permeability, protein-lipid interactions, along with "lipid-drug interactions, protein–ligand interactions, and protein structure and dynamics."

  3. Protein–lipid interaction - Wikipedia

    en.wikipedia.org/wiki/Proteinlipid_interaction

    Protein–lipid interaction is the influence of membrane proteins on the lipid physical state or vice versa.. The questions which are relevant to understanding of the structure and function of the membrane are: 1) Do intrinsic membrane proteins bind tightly to lipids (see annular lipid shell), and what is the nature of the layer of lipids adjacent to the protein?

  4. Protein–ligand docking - Wikipedia

    en.wikipedia.org/wiki/Protein–ligand_docking

    Coarse-grained models are often implemented in the case of protein-peptide docking, as they frequently involve large-scale conformation transitions of the protein receptor. [7] [8] AutoDock is one of the computational tools frequently used to model the interactions between proteins and ligands during the drug discovery process. Although the ...

  5. List of protein structure prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_protein_structure...

    Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.

  6. Protein–protein interaction prediction - Wikipedia

    en.wikipedia.org/wiki/Proteinprotein...

    Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex ...

  7. Macromolecular docking - Wikipedia

    en.wikipedia.org/wiki/Macromolecular_docking

    Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes. [1] The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism.

  8. List of protein secondary structure prediction programs

    en.wikipedia.org/wiki/List_of_protein_secondary...

    List of notable protein secondary structure prediction programs. Name Method description Type Link Initial release RaptorX-SS8

  9. PSIPRED - Wikipedia

    en.wikipedia.org/wiki/PSIPRED

    PSI-blast based secondary structure PREDiction (PSIPRED) is a method used to investigate protein structure. It uses artificial neural network machine learning methods in its algorithm. [ 2 ] [ 3 ] [ 4 ] It is a server-side program, featuring a website serving as a front-end interface, which can predict a protein's secondary structure ( beta ...