Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences

AD Bochevarov, E Harder, TF Hughes… - … Journal of Quantum …, 2013 - Wiley Online Library
Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure
predictions for molecular systems of medium and large size. Jaguar focuses on …

Protonation and pK changes in protein–ligand binding

AV Onufriev, E Alexov - Quarterly reviews of biophysics, 2013 - cambridge.org
Formation of protein–ligand complexes causes various changes in both the receptor and the
ligand. This review focuses on changes in pK and protonation states of ionizable groups that …

A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2

R Islam, MR Parves, AS Paul, N Uddin… - Journal of …, 2021 - Taylor & Francis
The main protease of SARS-CoV-2 is one of the important targets to design and develop
antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the …

Putative inhibitors of SARS-CoV-2 main protease from a library of marine natural products: a virtual screening and molecular modeling study

D Gentile, V Patamia, A Scala, MT Sciortino, A Piperno… - Marine drugs, 2020 - mdpi.com
The current emergency due to the worldwide spread of the COVID-19 caused by the new
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for …

Structure-and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound

Y Guo, L Alvigini, M Trajkovic… - Nature …, 2022 - nature.com
Various 4-alkylphenols can be easily obtained through reductive catalytic fractionation of
lignocellulosic biomass. Selective dehydrogenation of 4-n-propylguaiacol results in the …

Flexibility regulation of loops surrounding the tunnel entrance in cytochrome P450 enhanced substrate access substantially

Z Li, S Meng, K Nie, U Schwaneberg, MD Davari… - ACS …, 2022 - ACS Publications
In recent years, the engineering of flexible loops to improve enzyme properties has gained
attention in biocatalysis. Herein, we report a loop engineering strategy to improve the …

Assessment of antiviral potencies of cannabinoids against SARS-CoV-2 using computational and in vitro approaches

V Raj, JG Park, KH Cho, P Choi, T Kim, J Ham… - International journal of …, 2021 - Elsevier
Effective treatment choices to the severe acute respiratory syndrome coronavirus-2 (SARS-
CoV-2) are limited because of the absence of effective target-based therapeutics. The main …

ProteinsPlus: a web portal for structure analysis of macromolecules

R Fährrolfes, S Bietz, F Flachsenberg… - Nucleic acids …, 2017 - academic.oup.com
With currently more than 126 000 publicly available structures and an increasing growth
rate, the Protein Data Bank constitutes a rich data source for structure-driven research in …

Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic …

A Parihar, ZF Sonia, F Akter, MA Ali, FT Hakim… - Computers in Biology …, 2022 - Elsevier
The ongoing COVID-19 pandemic has affected millions of people worldwide and caused
substantial socio-economic losses. Few successful vaccine candidates have been approved …

Designing of a multi-epitope vaccine against the structural proteins of marburg virus exploiting the immunoinformatics approach

SA Sami, KKS Marma, S Mahmud, MAN Khan… - ACS …, 2021 - ACS Publications
Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with
flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with …