Motivation: Recent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).
Results: Ensembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.
Availability: dinc-covid.kavrakilab.org.
Supplementary Information: Details on methods for ensemble generation and docking are provided as supplementary data online.
Contact: geancarlo.zanatta@ufc.br , kavraki@rice.edu.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836118 | PMC |
| http://dx.doi.org/10.1101/2021.01.21.427315 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Impact of SARS-CoV-2 variants on viral infectivity and the role of the renin-angiotensin-aldosterone system.
Hypertens Res
January 2025
Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
Balance between Protective vs. Exacerbating Effects of ACEIs and ARBs in Omicron Variant Infections. The spike protein on the surface of the Omicron variant has a high affinity for ACE2, making it more prone to enter cells and induce ACE2 downregulation.
View Article and Find Full Text PDFRecombinant XBB.1.5 boosters induce robust neutralization against KP.2- and KP.3-included JN.1 sublineages.
Signal Transduct Target Ther
January 2025
Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, People's Republic of China.
The newly emerged variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) demonstrate resistance to present therapeutic antibodies as well as the capability to evade vaccination-elicited antibodies. JN.1 sublineages were demonstrated as one of the most immune-evasive variants, showing higher neutralization resistance compared to XBB.
View Article and Find Full Text PDFEffectiveness of Frequent Point-of-Care Molecular COVID-19 Surveillance in a Rural Workplace: Nonrandomized Controlled Clinical Trial Among Miners.
JMIR Public Health Surveill
January 2025
Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, United States.
Background: Numerous studies have assessed the risk of SARS-CoV-2 exposure and infection among health care workers during the pandemic. However, far fewer studies have investigated the impact of SARS-CoV-2 on essential workers in other sectors. Moreover, guidance for maintaining a safely operating workplace in sectors outside of health care remains limited.
View Article and Find Full Text PDFLow Neutralization of SARS-CoV-2 Omicron BA5248, XBB15 and JN1 by Homologous Booster and Breakthrough Infection.
J Med Virol
February 2025
Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, P. R. China.
Immunity against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be induced through either infection with the virus or vaccination, providing protection against reinfection or reducing the risk of severe clinical outcomes. In this study, we recruited 172 volunteers who received different vaccination regimens, including 124 individuals who had recovered from breakthrough infections caused by the Omicron variant (27 with 2 doses, 49 with 3 doses, and 48 with 4 doses) and 48 healthy donors who did not experience breakthrough infections (all of whom received a fourth dose during the infection wave). We measured neutralizing antibody levels against Omicron BA.
View Article and Find Full Text PDFSafety and immunogenicity of Ad26.COV2.S in adolescents: Phase 2 randomized clinical trial.
Hum Vaccin Immunother
December 2025
Crucell Integration, Janssen Research and Development, Beerse, Belgium.
We conducted a randomized, Phase 2 trial to assess the safety and humoral immunogenicity of reduced doses/dose volume of the standard dose of Ad26.COV2.S COVID-19 vaccine (5 × 10 viral particles [vp]) in healthy adolescents aged 12-17 years.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!