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  2. Protein structure prediction - Wikipedia

    en.wikipedia.org/wiki/Protein_structure_prediction

    An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).

  3. Protein secondary structure - Wikipedia

    en.wikipedia.org/wiki/Protein_secondary_structure

    Predicting protein tertiary structure from only its amino sequence is a very challenging problem (see protein structure prediction), but using the simpler secondary structure definitions is more tractable. Early methods of secondary-structure prediction were restricted to predicting the three predominate states: helix, sheet, or random coil.

  4. GOR method - Wikipedia

    en.wikipedia.org/wiki/GOR_method

    The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17 ...

  5. Chou–Fasman method - Wikipedia

    en.wikipedia.org/wiki/Chou–Fasman_method

    The Chou–Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman. [ 1 ] [ 2 ] [ 3 ] The method is based on analyses of the relative frequencies of each amino acid in alpha helices , beta sheets , and turns based on known protein ...

  6. Secondary structure prediction - Wikipedia

    en.wikipedia.org/wiki/Secondary_structure_prediction

    For proteins, this means predicting the formation of protein structures such as alpha helices and beta strands, while for nucleic acids it means predicting the formation of nucleic acid structures like helixes and stem-loop structures through base pairing and base stacking interactions. Secondary structure prediction can refer to:

  7. Ribbon diagram - Wikipedia

    en.wikipedia.org/wiki/Ribbon_diagram

    Ribbon diagram of myoglobin bound to haem (sticks) and oxygen (red spheres) (Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organisation of the protein backbone in 3D and ...

  8. PSIPRED - Wikipedia

    en.wikipedia.org/wiki/PSIPRED

    The three final output nodes deliver a score for each secondary structure element for the central position of the window. Using the secondary structure with the highest score, PSIPRED generates the protein prediction. [9] The Q3 value is the fraction of residues predicted correctly in the secondary structure states, namely helix, strand, and ...

  9. Graphical models for protein structure - Wikipedia

    en.wikipedia.org/wiki/Graphical_models_for...

    Graphical models have become powerful frameworks for protein structure prediction, proteinprotein interaction, and free energy calculations for protein structures. Using a graphical model to represent the protein structure allows the solution of many problems including secondary structure prediction, protein-protein interactions, protein-drug interaction, and free energy calculations.