Literature DB >> 33100917

Biomolecular Simulations in the Time of COVID19, and After.

Rommie E Amaro1, Adrian J Mulholland2.   

Abstract

COVID19 has changed life for people worldwide. Despite lockdowns globally, computational research has pressed on, working remotely and collaborating virtually on research questions in COVID19 and the virus it is caused by, SARS-CoV-2. Molecular simulations can help to characterize the function of viral and host proteins and have the potential to contribute to the search for vaccines and treatments. Changes in the modus operandi of research groups include broader adoption of the use of preprint servers, earlier and more open sharing of methods, models, and data, the use of social media to rapidly disseminate information, online seminars, and cloud-based virtual collaboration. Research funders and computing providers worldwide recognized the need to provide rapid and significant access to computational architectures. In this review, we discuss how the interplay of all of these factors is influencing the impact - both potential and realized - of biomolecular simulations in the fight against SARS-CoV-2.

Entities:  

Keywords:  COVID19; COVID19 HPC Consortium; HPC; SARS-CoV-2; bioRxiv deposition; computational biophysics; glycans; molecular dynamics simulations; open access; protease; spike protein

Year:  2020        PMID: 33100917      PMCID: PMC7584139          DOI: 10.1109/MCSE.2020.3024155

Source DB:  PubMed          Journal:  Comput Sci Eng        ISSN: 1521-9615            Impact factor:   2.080


  5 in total

1.  Crowdsourcing drug discovery for pandemics.

Authors:  John Chodera; Alpha A Lee; Nir London; Frank von Delft
Journal:  Nat Chem       Date:  2020-07       Impact factor: 24.427

2.  A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19.

Authors:  Rommie E Amaro; Adrian J Mulholland
Journal:  J Chem Inf Model       Date:  2020-05-01       Impact factor: 4.956

3.  Neuropilin-1 is a host factor for SARS-CoV-2 infection.

Authors:  James L Daly; Boris Simonetti; Katja Klein; Kai-En Chen; Maia Kavanagh Williamson; Carlos Antón-Plágaro; Deborah K Shoemark; Lorena Simón-Gracia; Michael Bauer; Reka Hollandi; Urs F Greber; Peter Horvath; Richard B Sessions; Ari Helenius; Julian A Hiscox; Tambet Teesalu; David A Matthews; Andrew D Davidson; Brett M Collins; Peter J Cullen; Yohei Yamauchi
Journal:  Science       Date:  2020-10-20       Impact factor: 63.714

4.  In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.

Authors:  Beata Turoňová; Mateusz Sikora; Christoph Schürmann; Wim J H Hagen; Sonja Welsch; Florian E C Blanc; Sören von Bülow; Michael Gecht; Katrin Bagola; Cindy Hörner; Ger van Zandbergen; Jonathan Landry; Nayara Trevisan Doimo de Azevedo; Shyamal Mosalaganti; Andre Schwarz; Roberto Covino; Michael D Mühlebach; Gerhard Hummer; Jacomine Krijnse Locker; Martin Beck
Journal:  Science       Date:  2020-08-18       Impact factor: 47.728

5.  Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.

Authors:  Peng Zhao; Jeremy L Praissman; Oliver C Grant; Yongfei Cai; Tianshu Xiao; Katelyn E Rosenbalm; Kazuhiro Aoki; Benjamin P Kellman; Robert Bridger; Dan H Barouch; Melinda A Brindley; Nathan E Lewis; Michael Tiemeyer; Bing Chen; Robert J Woods; Lance Wells
Journal:  Cell Host Microbe       Date:  2020-08-24       Impact factor: 21.023

  5 in total
  10 in total

1.  The flexibility of ACE2 in the context of SARS-CoV-2 infection.

Authors:  Emilia P Barros; Lorenzo Casalino; Zied Gaieb; Abigail C Dommer; Yuzhang Wang; Lucy Fallon; Lauren Raguette; Kellon Belfon; Carlos Simmerling; Rommie E Amaro
Journal:  Biophys J       Date:  2020-11-13       Impact factor: 4.033

2.  Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide.

Authors:  George Khelashvili; Ambrose Plante; Milka Doktorova; Harel Weinstein
Journal:  Biophys J       Date:  2021-02-23       Impact factor: 4.033

3.  Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells.

Authors:  Liqun Zhang; Santosh K Ghosh; Shrikanth C Basavarajappa; Jeannine Muller-Greven; Jackson Penfield; Ann Brewer; Parameswaran Ramakrishnan; Matthias Buck; Aaron Weinberg
Journal:  bioRxiv       Date:  2021-01-07

Review 4.  Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: lessons from the pandemic and preparing for future health crises.

Authors:  Natesh Singh; Bruno O Villoutreix
Journal:  Comput Struct Biotechnol J       Date:  2021-04-26       Impact factor: 7.271

5.  Molecular Simulations suggest Vitamins, Retinoids and Steroids as Ligands of the Free Fatty Acid Pocket of the SARS-CoV-2 Spike Protein*.

Authors:  Deborah K Shoemark; Charlotte K Colenso; Christine Toelzer; Kapil Gupta; Richard B Sessions; Andrew D Davidson; Imre Berger; Christiane Schaffitzel; James Spencer; Adrian J Mulholland
Journal:  Angew Chem Int Ed Engl       Date:  2021-02-22       Impact factor: 16.823

6.  HBD-2 binds SARS-CoV-2 RBD and blocks viral entry: Strategy to combat COVID-19.

Authors:  Liqun Zhang; Santosh K Ghosh; Shrikanth C Basavarajappa; Yinghua Chen; Pravesh Shrestha; Jackson Penfield; Ann Brewer; Parameswaran Ramakrishnan; Matthias Buck; Aaron Weinberg
Journal:  iScience       Date:  2022-02-02

Review 7.  Applications of Molecular Dynamics Simulation in Protein Study.

Authors:  Siddharth Sinha; Benjamin Tam; San Ming Wang
Journal:  Membranes (Basel)       Date:  2022-08-29

Review 8.  Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches.

Authors:  Antonio Francés-Monerris; Cécilia Hognon; Tom Miclot; Cristina García-Iriepa; Isabel Iriepa; Alessio Terenzi; Stéphanie Grandemange; Giampaolo Barone; Marco Marazzi; Antonio Monari
Journal:  J Proteome Res       Date:  2020-10-29       Impact factor: 4.466

9.  Distributed messaging and light streaming system for combating pandemics: A case study on spatial analysis of COVID-19 Geo-tagged Twitter dataset.

Authors:  Yavuz Melih Özgüven; Süleyman Eken
Journal:  J Ambient Intell Humaniz Comput       Date:  2021-06-10

10.  GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses.

Authors:  Sang Hoon Kim; Fiona L Kearns; Mia A Rosenfeld; Lorenzo Casalino; Micah J Papanikolas; Carlos Simmerling; Rommie E Amaro; Ronit Freeman
Journal:  ACS Cent Sci       Date:  2021-12-15       Impact factor: 14.553

  10 in total

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