Jun 9, 2020Paper

Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement

BioRxiv : the Preprint Server for Biology
Lim Heo, Michael Feig

Abstract

Protein structures are crucial for understanding their biological activities. Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need to understand the biological behavior of the virus and provide a basis for developing effective therapies. Since the proteome of the virus was determined, some of the protein structures could be determined experimentally, and others were predicted via template-based modeling approaches. However, tertiary structures for several proteins are still not available from experiment nor they could be accurately predicted by template-based modeling because of lack of close homolog structures. Previous efforts to predict structures for these proteins include efforts by DeepMind and the Zhang group via machine learning-based structure prediction methods, i.e. AlphaFold and C-I-TASSER. However, the predicted models vary greatly and have not yet been subjected to refinement. Here, we are reporting new predictions from our in-house structure prediction pipeline. The pipeline takes advantage of inter-residue contact predictions from trRosetta, a machine learning-based method. The predicted models were further improved by applying molecular dynamics simulation-...Continue Reading

Citations

Aug 23, 2020·Pathogens·Sameer MohammadShuja Shafi Malik
Dec 22, 2020·Briefings in Bioinformatics·Vaishali P WamanChristine Orengo
Dec 17, 2020·JMIR Medical Informatics·Hafsa Bareen SyedaFeliciano Yu
Apr 20, 2021·Informatics in Medicine Unlocked·Mohammad Sadeq MottaqiHedieh Sajedi
Dec 24, 2020·Journal of Biomolecular Structure & Dynamics·Rumana MahtarinMohammad A Halim
Jun 5, 2021·The Journal of Physical Chemistry Letters·Anna PavlovaJames C Gumbart
Jun 19, 2021·PeerJ. Computer Science·Vijay KumarRobertas Damaševičius
Jul 3, 2021·Diagnostics·Nora El-RashidyShaker El-Sappagh
Aug 10, 2021·The Journal of Physical Chemistry. B·Asis K JanaUlrich H E Hansmann
Sep 15, 2021·Molecular Systems Biology·Seán I O'DonoghueBurkhard Rost
Sep 17, 2021·Journal of Chemical Information and Modeling·Kornel OzvoldikElmar Krieger
Sep 21, 2021·Faraday Discussions·Viviana Monje-Galvan, Gregory A Voth
Nov 27, 2021·Faraday Discussions·Patricia Bassereau
Dec 21, 2021·The Journal of Physical Chemistry Letters·Logan Thrasher CollinsAnkush Singhal

❮ Previous
Next ❯

Related Concepts

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.