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CAMEO performs blind assessment of protein structure prediction techniques based on the weekly releases of newly determined experimental structures by the Protein Databank (PDB). The amino acid sequences of soon to be released protein structures are submitted to the participating web-servers. The web-servers return their predictions to CAMEO ...
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.
Swiss-model (stylized as SWISS-MODEL) is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. [1] [2] As of 2024, homology modeling is the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology (or comparative ...
A chemical graph generator is a software package to generate computer representations of chemical structures adhering to certain boundary conditions. The development of such software packages is a research topic of cheminformatics .
It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers. [1] HELM was developed by a consortium of pharmaceutical companies in what is known as the Pistoia Alliance. Development began in 2008. In 2012 the notation was published openly and for ...
Secondary structure [4] [5] α-Helices Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides. β-Strands Arrows with thickness, about one-quarter as thick as they are wide, showing direction and twist of the strand from amino to carboxy end. β-sheets are seen as unified because neighboring strands twist in unison.
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).
A typical PDB file describing a protein consists of hundreds to thousands of lines like the following (taken from a file describing the structure of a synthetic collagen-like peptide): HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE TITLE 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY