Material associated with our PLoS One paper on DeepCDpred.
DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205214 Descriptions and links to the software used to create the input feature vector can be found at the end of the supplementary material of the above linked article.
Network Training Script The python script for training the neural network is given in the file train network.py in this repository. Rosetta Scripts Parameter settings in the Rosetta protocol file: The Rosetta script that is used to generate structures via Abinitio relax is given in the file flags for rosetta ab initio. (flags_for_rosetta_ab_initio)
Shuangxi Ji Contributed equally to this work with: Shuangxi Ji, Tuğçe Oruç
ROLES Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Visualization, Writing – review & editing
AFFILIATION School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom
Tuğçe Oruç Contributed equally to this work with: Shuangxi Ji, Tuğçe Oruç
ROLES Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing
AFFILIATION School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom
Liam Mead ROLES Formal analysis, Methodology, Writing – review & editing
AFFILIATION School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom
Muhammad Fayyaz Rehman ROLES Formal analysis, Writing – review & editing
Current address: Department of Chemistry, University of Sargodha, Sargodha, Pakistan
AFFILIATION School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom
Christopher Morton Thomas ROLES Conceptualization, Funding acquisition, Supervision, Writing – review & editing
AFFILIATION School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom
Sam Butterworth ROLES Conceptualization, Supervision, Writing – review & editing
AFFILIATIONS School of Biosciences, University of Birmingham, Edgbaston Birmingham, B15 2TT, United Kingdom, Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PL, United Kingdom
ORCID logohttp://orcid.org/0000-0002-6549-3753
Peter James Winn ROLES Conceptualization, Methodology, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing