EvoDesign protocols

View EvoDesign computational protocol

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EvoDesign specifications

Information


Unique identifier OMICS_10811
Name EvoDesign
Interface Web user interface
Restrictions to use None
Input data Scaffold structure (C-alpha only or full-atomic)
Input format PDB format
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publication for EvoDesign

EvoDesign in pipeline

2013
PMCID: 3812052
PMID: 24204234
DOI: 10.1371/journal.pcbi.1003298

[…] parameters in and (w1–5) were determined on a set of 625 non-redundant training proteins that are non-homologous to the test set and case study proteins (see http://zhanglab.ccmb.med.umich.edu/evodesign/list625.txt). for w1–3 in , the weights are decided by the relative accuracy of the individual feature predictions, i.e. w1 = c*ass, w2 = c*asa, w3 = c*ata, where ass, asa and ata […]


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EvoDesign in publications

 (2)
PMCID: 5482196
PMID: 28167677
DOI: 10.1042/BSR20160179

[…] backbone flexibility is also incorporated into the calculations []., a compelling number of programs such as protein wisdom [], hostdesigner [], metalsearch [], core [], rosettadesign [], evodesign [], rosettabackrub [], ipro (optgraft procedure) [], pyrosetta [] has been in use for de novo protein design (). these software provide in silico workbenches for the design of novel, stable […]

PMCID: 3962155
PMID: 24688747
DOI: 10.5936/csbj.201308007

[…] characteristics of a designed structure. most current protein design methods rely on physics-based force fields to search for low free-energy states. recently, mitra et al. [] developed a method, evodesign, to design ideal protein sequences for given scaffolds. at first, evodesign collects a set of proteins with similar folds from the pdb data, by a structural alignment with a query […]


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EvoDesign institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

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