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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.
I-TASSER is a template-based method for protein structure and function prediction. [1] The pipeline consists of six consecutive steps: 1, Secondary structure prediction by PSSpred; 2, Template detection by LOMETS [6] 3, Fragment structure assembly using replica-exchange Monte Carlo simulation [7]
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).
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
An email is sent to the user together with a link to a web page of results. RaptorX Server currently generates the following results: 3-state and 8-state secondary structure prediction, sequence-template alignment, 3D structure prediction, solvent accessibility prediction, disorder prediction and binding site prediction.
The Swiss-model Workspace integrates programs and databases required for protein structure prediction and modelling in a web-based workspace. Depending on the complexity of the modelling task, different modes of use can be applied, in which the user has different levels of control over individual modelling steps: automated mode, alignment mode, and project mode.
Secondary structure-related. Based on an assumption that protein sequences that are able to form β-arcades are amyloidogenic. sequence - Amyloidogenic regions Amyload [38] 2015 Web Server - Comprec (currently offline) Consensus method: sequence - Overall generic and amyloidogenic regions SolubiS [39] [40] 2016 Web Server - SolubiS: 3D ...
Phyre and Phyre2 are the successors to the 3D-PSSM [14] protein structure prediction system which has over 1,400 citations to date. [15] 3D-PSSM was designed and developed by Lawrence Kelley [16] and Bob MacCallum [17] in the Biomolecular modelling Lab [18] at the Cancer Research UK.