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pyconsFold :
pyconsFold : a fast and easy tool for modeling and docking using distance predictions
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- Lamb, John (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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- Elofsson, Arne (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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(creator_code:org_t)
- 2021-07-08
- 2021
- Engelska.
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:21, s. 3959-3960
- Relaterad länk:
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https://doi.org/10.1...
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Motivation: Contact predictions within a protein have recently become a viable method for accurate prediction of protein structure. Using predicted distance distributions has been shown in many cases to be superior to only using a binary contact annotation. Using predicted interprotein distances has also been shown to be able to dock some protein dimers.Results: Here, we present pyconsFold. Using CNS as its underlying folding mechanism and predicted contact distance it outperforms regular contact prediction-based modeling on our dataset of 210 proteins. It performs marginally worse than the state-of-the-art pyRosetta folding pipeline but is on average about 20 times faster per model. More importantly pyconsFold can also be used as a fold-and-dock protocol by using predicted interprotein contacts/distances to simultaneously fold and dock two protein chains.Availability and implementation: pyconsFold is implemented in Python 3 with a strong focus on using as few dependencies as possible for longevity. It is available both as a pip package in Python 3 and as source code on GitHub and is published under the GPLv3 license. The data underlying this article together with source code are available on github, at https://github.com/johnlamb/pyconsfold.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
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- ref (ämneskategori)
- art (ämneskategori)
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