Carmine Talarico
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View article: PANTHER - Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression
PANTHER - Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression Open
Although protein-RNA interactions are crucial for many biological processes, predicting their binding free energies (ΔG) is a challenging task due to limited available experimental data and the complexity of these interactions. To address …
View article: GENEOnet: a breakthrough in protein binding pocket detection using group equivariant non-expansive operators
GENEOnet: a breakthrough in protein binding pocket detection using group equivariant non-expansive operators Open
Structure-based virtual screening approaches like molecular docking rely on accurately identifying and precisely calculating binding pockets to efficiently search for potential ligands. In this paper, we introduce GENEOnet, a machine learn…
View article: Dual-Site Inhibition of SARS-CoV-2 RNA-Dependent RNA Polymerase by Small Molecules Able to Block Viral Replication Identified through a Computer-Aided Drug Discovery Approach
Dual-Site Inhibition of SARS-CoV-2 RNA-Dependent RNA Polymerase by Small Molecules Able to Block Viral Replication Identified through a Computer-Aided Drug Discovery Approach Open
Since its emergence in late 2019, SARS-CoV-2, the causative agent of COVID-19, has continued to spread globally, with more than 7 million reported deaths as of March 2025. Among the viral nonstructural proteins, nsp12 serves as the RNA-dep…
View article: GENEOnet: statistical analysis supporting explainability and trustworthiness
GENEOnet: statistical analysis supporting explainability and trustworthiness Open
Group Equivariant Non-Expansive Operators (GENEOs) have emerged as mathematical tools for constructing networks for Machine Learning and Artificial Intelligence. Recent findings suggest that such models can be inserted within the domain of…
View article: Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors
Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors Open
Tryptase is a tetrameric serine protease and a key component of mast cell granules. Here, we explored an integrated approach to characterize tryptase ligands, combining novel experimental binding studies using Surface Plasmon Resonance, wi…
View article: Novel method for prioritizing protein binding sites using pocket analysis and MD simulations
Novel method for prioritizing protein binding sites using pocket analysis and MD simulations Open
Successful virtual screening of therapeutically relevant proteins depends on selecting optimal protein structures and accurately identifying druggable binding sites. This study presents a novel methodology that combines pocket analysis, mo…
View article: Cys44 of SARS-CoV-2 3CLpro affects its catalytic activity
Cys44 of SARS-CoV-2 3CLpro affects its catalytic activity Open
SARS-CoV-2 encodes a 3C-like protease (3CLpro) that is essential for viral replication. This cysteine protease cleaves viral polyproteins to release functional nonstructural proteins, making it a prime target for antiviral drug development…
View article: LIGATE - LIgand Generator and portable drug discovery platform AT Exascale
LIGATE - LIgand Generator and portable drug discovery platform AT Exascale Open
The COVID-19 pandemic demonstrates that a top priority for society, now and in the future, is to be able to respond quickly to diseases with effective treatments. Among the new tools that pharmaceutical industries and researchers have in t…
View article: Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative
Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative Open
Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rar…
View article: SiteMap pockets for the PDBbind dataset
SiteMap pockets for the PDBbind dataset Open
This dataset includes the protein pockets identified by using the SITEMAP approach [SITEMAP] for the PDBbind v.2020 dataset. Only the proteins that were automatically processed by the tool, without generating any error, are included here. …
View article: SiteMap pockets for the PDBbind dataset
SiteMap pockets for the PDBbind dataset Open
This dataset includes the protein pockets identified by using the SITEMAP approach [SITEMAP] for the PDBbind v.2020 dataset. Only the proteins that were automatically processed by the tool, without generating any error, are included here. …
View article: Structure of human TRPM8 channel
Structure of human TRPM8 channel Open
This repository includes the following source datasets: 1. modeling.zip Modeling of icilin binding to HsTRPM8 (Figure 3e, 3f, 3g, 3h) - HsTRPM8-KX7_opt.pdb: original pose (Figure 3e, 3f) - HsTRPM8-KX7_opt_rotated.pdb: rotates pose (Figure …
View article: Structure of human TRPM8 channel
Structure of human TRPM8 channel Open
This repository includes the following source datasets: 1. modeling.zip Modeling of icilin binding to HsTRPM8 (Figure 3e, 3f, 3g, 3h) - HsTRPM8-KX7_opt.pdb: original pose (Figure 3e, 3f) - HsTRPM8-KX7_opt_rotated.pdb: rotates pose (Figure …
View article: A community effort in SARS‐CoV‐2 drug discovery
A community effort in SARS‐CoV‐2 drug discovery Open
The COVID‐19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small‐molecule drugs that are widely available, including i…
View article: MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions
MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions Open
Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organ…
View article: Conformational response to ligand binding of TMPRSS2, a protease involved in SARS‐CoV‐2 infection: Insights through computational modeling
Conformational response to ligand binding of TMPRSS2, a protease involved in SARS‐CoV‐2 infection: Insights through computational modeling Open
Thanks to the considerable research which has been undertaken in the last few years to improve our understanding of the biology and mechanism of action of SARS‐CoV‐2, we know how the virus uses its surface spike protein to infect host cell…
View article: DHFR Inhibitors Display a Pleiotropic Anti-Viral Activity against SARS-CoV-2: Insights into the Mechanisms of Action
DHFR Inhibitors Display a Pleiotropic Anti-Viral Activity against SARS-CoV-2: Insights into the Mechanisms of Action Open
During the COVID-19 pandemic, drug repurposing represented an effective strategy to obtain quick answers to medical emergencies. Based on previous data on methotrexate (MTX), we evaluated the anti-viral activity of several DHFR inhibitors …
View article: Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale Open
Today digital revolution is having a dramatic impact on the pharmaceutical\nindustry and the entire healthcare system. The implementation of machine\nlearning, extreme-scale computer simulations, and big data analytics in the\ndrug design …
View article: A community effort to discover small molecule SARS-CoV-2 inhibitors
A community effort to discover small molecule SARS-CoV-2 inhibitors Open
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including i…
View article: DHFR Inhibitors Display a Pleiotropic Anti-viral Activity Against SARS-CoV-2: Insights Into the Mechanisms of Action
DHFR Inhibitors Display a Pleiotropic Anti-viral Activity Against SARS-CoV-2: Insights Into the Mechanisms of Action Open
During COVID-19 pandemic, drug repurposing represented an effective strategy to obtain quick answers to medical emergencies. Basing on previous data on Methotrexate (MTX), we evaluated the anti-viral activity of several DHFR inhibitors in …
View article: Structure of human TRPM8 channel
Structure of human TRPM8 channel Open
TRPM8 is a calcium ion channel that is activated by multiple factors, such as temperature, voltage, pressure, and osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathol…
View article: The SARS-CoV-2 spike protein binds and modulates estrogen receptors
The SARS-CoV-2 spike protein binds and modulates estrogen receptors Open
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 as its primary infection mechanism. Interactions between S and endogenous proteins occur after infection but are not w…
View article: The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2
The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2 Open
A large number of SARS-CoV-2 mutations in a short period of time has driven scientific research related to vaccines, new drugs, and antibodies to combat the new variants of the virus. Herein, we present a web portal containing the structur…
View article: Structure of human TRPM8 channel
Structure of human TRPM8 channel Open
SUMMARY TRPM8 is a calcium ion channel that is activated by multiple factors, such as temperature, voltage, pressure, and osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for severa…
View article: Relevance of the viral Spike protein/cellular Estrogen Receptor-α interaction for endothelial-based coagulopathy induced by SARS-CoV-2
Relevance of the viral Spike protein/cellular Estrogen Receptor-α interaction for endothelial-based coagulopathy induced by SARS-CoV-2 Open
Severe coagulopathy has been observed at the level of the microcirculation in several organs including lungs, heart and kidneys in patients with COVID-19, and in a minority of subjects receiving the SARS-CoV-2 vaccine. Various mechanisms h…
View article: Computational Insights into the Sequence-Activity Relationships of the NGF(1–14) Peptide by Molecular Dynamics Simulations
Computational Insights into the Sequence-Activity Relationships of the NGF(1–14) Peptide by Molecular Dynamics Simulations Open
The Nerve Growth Factor (NGF) belongs to the neurothrophins protein family involved in the survival of neurons in the nervous system. The interaction of NGF with its high-affinity receptor TrkA mediates different cellular pathways related …