Ensemble learning from ensemble docking: Revisiting the optimum ensemble size problem

S Mohammadi, Z Narimani, M Ashouri, R Firouzi… - Scientific reports, 2022 - nature.com
Despite considerable advances obtained by applying machine learning approaches in
protein–ligand affinity predictions, the incorporation of receptor flexibility has remained an …

Use of the complementarity principle in docking procedures: A new approach for evaluating the correctness of binding poses

H Rimac, M Grishina, V Potemkin - Journal of chemical information …, 2021 - ACS Publications
Even though the first docking procedures were developed almost 40 years ago, they are still
under intense development, alongside with their validation. In this article, we are proposing …

How well do semiempirical QM methods describe the structure of proteins?

J Řezáč, JJP Stewart - The Journal of Chemical Physics, 2023 - pubs.aip.org
Semiempirical quantum-mechanical (QM) computational methods are an increasingly
popular tool for the study of biomolecular systems. They were, however, developed and …

Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery

R Firouzi, M Ashouri… - … : Structure, Function, and …, 2022 - Wiley Online Library
An attractive drug target to combat COVID‐19 is the main protease (Mpro) because of its key
role in the viral life cycle by processing the polyproteins translated from the viral RNA …

Identification of Catechins' Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

R Firouzi, S Sowlati-Hashjin, C Chávez-García… - International Journal of …, 2023 - mdpi.com
The assembly of the amyloid-β peptide (A β) into toxic oligomers and fibrils is associated
with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct …

Identification of potential anti‐COVID‐19 drug leads from medicinal plants through virtual high‐throughput screening

R Firouzi, M Ashouri - ChemistrySelect, 2023 - Wiley Online Library
Natural compounds are widely used as attractive and valuable starting points for drug lead
discovery. The present study aims to identify phytochemical compounds found in medicinal …

Improving protein-ligand docking results using the Semiempirical quantum mechanics: testing on the PDBbind 2016 core set

Z Mohebbinia, R Firouzi… - Journal of Biomolecular …, 2023 - Taylor & Francis
Molecular docking techniques are routinely employed for predicting ligand binding
conformations and affinities in the in silico phase of the drug design and development …

Identification of Catechins Binding Pockets in Monomeric Aβ42 Through Ensemble Docking and MD Simulations

R Firouzi, S Sowlati-Hashjin, C Chávez-García… - BioRxiv, 2022 - biorxiv.org
The assembly of the Amyloid-β peptide (A β) into toxic oligomers and fibrils is associated
with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct …

Virtual Screening and binding mode analysis of selected FDA approved drugs against PLpro target: An effort to identify therapeutics to combat COVID-19

M Ashouri, R Firouzi - 2023 - chemrxiv.org
Papain-like protease (PLpro) is one of the most promising targets for anti-SARS-CoV drugs.
In this study, a bioactive library of FDA-approved drugs has virtually been screened using a …

[PDF][PDF] 510-MODELAGEM in silico DA INTERAÇÃO DO CONTAMINANTE 4-NONILFENOL COM A ENZIMA LACASE DE Pycnoporus cinnabarinus

RL da Silva Santos, F Motteran - researchgate.net
Os impactos advindos da urbanização e industrialização desenfreada no ecossistema e na
saúde humana têm despertado interesse e preocupação mundial principalmente no que diz …