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  1. Book ; Online: Chapter Ammonia emissions and fine particulate matter: some evidence in Lombardy

    Salis, Matteo / Zucchi, Andrea / FUSTA MORO, ALESSANDRO / Cameletti, Michela / GOLINI, Natalia / Ignaccolo, Rosaria

    (Proceedings e report)

    2023  

    Series title Proceedings e report
    Keywords Society & social sciences ; Spatio-temporal Kriging ; Random Forest ; Predictive modeling ; Air quality ; Agriculture emissions
    Language English
    Size 1 electronic resource (6 pages)
    Publisher Firenze University Press, Genova University Press
    Publishing place Florence
    Document type Book ; Online
    Note English
    HBZ-ID HT030381571
    ISBN 9791221501063
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.

    Pavan, Matteo / Moro, Stefano

    International journal of molecular sciences

    2023  Volume 24, Issue 5

    Abstract: Since its outbreak in December 2019, the COVID-19 pandemic has caused the death of more than 6.5 million people around the world. The high transmissibility of its causative agent, the SARS-CoV-2 virus, coupled with its potentially lethal outcome, ... ...

    Abstract Since its outbreak in December 2019, the COVID-19 pandemic has caused the death of more than 6.5 million people around the world. The high transmissibility of its causative agent, the SARS-CoV-2 virus, coupled with its potentially lethal outcome, provoked a profound global economic and social crisis. The urgency of finding suitable pharmacological tools to tame the pandemic shed light on the ever-increasing importance of computer simulations in rationalizing and speeding up the design of new drugs, further stressing the need for developing quick and reliable methods to identify novel active molecules and characterize their mechanism of action. In the present work, we aim at providing the reader with a general overview of the COVID-19 pandemic, discussing the hallmarks in its management, from the initial attempts at drug repurposing to the commercialization of Paxlovid, the first orally available COVID-19 drug. Furthermore, we analyze and discuss the role of computer-aided drug discovery (CADD) techniques, especially those that fall in the structure-based drug design (SBDD) category, in facing present and future pandemics, by showcasing several successful examples of drug discovery campaigns where commonly used methods such as docking and molecular dynamics have been employed in the rational design of effective therapeutic entities against COVID-19.
    MeSH term(s) Humans ; COVID-19 ; Pandemics ; SARS-CoV-2 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Drug Repositioning/methods ; Antiviral Agents/pharmacology
    Chemical Substances nirmatrelvir and ritonavir drug combination ; Antiviral Agents
    Language English
    Publishing date 2023-02-23
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24054401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Large languages, impossible languages and human brains.

    Moro, Andrea / Greco, Matteo / Cappa, Stefano F

    Cortex; a journal devoted to the study of the nervous system and behavior

    2023  Volume 167, Page(s) 82–85

    Abstract: We aim at offering a contribution to highlight the essential differences between Large Language Models (LLM) and the human language faculty. More explicitly, we claim that the existence of impossible languages for humans does not have any equivalent for ... ...

    Abstract We aim at offering a contribution to highlight the essential differences between Large Language Models (LLM) and the human language faculty. More explicitly, we claim that the existence of impossible languages for humans does not have any equivalent for LLM making them unsuitable models of the human language faculty, especially for a neurobiological point of view. The core part is preceded by two premises bearing on the distinction between machines and humans and the distinction between competence and performance.
    Language English
    Publishing date 2023-07-17
    Publishing country Italy
    Document type Journal Article
    ZDB-ID 280622-8
    ISSN 1973-8102 ; 0010-9452
    ISSN (online) 1973-8102
    ISSN 0010-9452
    DOI 10.1016/j.cortex.2023.07.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 687: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  4. Article ; Online: Targeting the I7L Protease: A Rational Design for Anti-Monkeypox Drugs?

    Dodaro, Andrea / Pavan, Matteo / Moro, Stefano

    International journal of molecular sciences

    2023  Volume 24, Issue 8

    Abstract: The latest monkeypox virus outbreak in 2022 showcased the potential threat of this viral zoonosis to public health. The lack of specific treatments against this infection and the success of viral protease inhibitors-based treatments against HIV, ... ...

    Abstract The latest monkeypox virus outbreak in 2022 showcased the potential threat of this viral zoonosis to public health. The lack of specific treatments against this infection and the success of viral protease inhibitors-based treatments against HIV, Hepatitis C, and SARS-CoV-2, brought the monkeypox virus I7L protease under the spotlight as a potential target for the development of specific and compelling drugs against this emerging disease. In the present work, the structure of the monkeypox virus I7L protease was modeled and thoroughly characterized through a dedicated computational study. Furthermore, structural information gathered in the first part of the study was exploited to virtually screen the DrugBank database, consisting of drugs approved by the Food and Drug Administration (FDA) and clinical-stage drug candidates, in search for readily repurposable compounds with similar binding features as TTP-6171, the only non-covalent I7L protease inhibitor reported in the literature. The virtual screening resulted in the identification of 14 potential inhibitors of the monkeypox I7L protease. Finally, based on data collected within the present work, some considerations on developing allosteric modulators of the I7L protease are reported.
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Pharmaceutical Preparations ; Peptide Hydrolases/metabolism ; Molecular Docking Simulation ; Viral Nonstructural Proteins/metabolism ; Cysteine Endopeptidases/metabolism ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Antiviral Agents/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; Protease Inhibitors/chemistry ; Molecular Dynamics Simulation ; Drug Repositioning/methods
    Chemical Substances Pharmaceutical Preparations ; Peptide Hydrolases (EC 3.4.-) ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Antiviral Agents ; Protease Inhibitors
    Language English
    Publishing date 2023-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24087119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: The dataset of the CLU lichen herbarium (Calabria, Italy).

    Conti, Matteo / Martellos, Stefano / Moro, Andrea / Nimis, Pier Luigi / Puntillo, Domenico

    Biodiversity data journal

    2024  Volume 12, Page(s) e116965

    Abstract: Background: Calabria, the southernmost tip of the Italian Peninsula, is a biogeographically very interesting region for lichenologists, characterised by the abundance of oceanic and suboceanic species with subtropical affinities, but also by the ... ...

    Abstract Background: Calabria, the southernmost tip of the Italian Peninsula, is a biogeographically very interesting region for lichenologists, characterised by the abundance of oceanic and suboceanic species with subtropical affinities, but also by the presence of the southernmost outposts of several boreal species on the highest peaks. The lichen biota of Calabria, which began to be intensively studied only from the 1980s, hosts more than 1000 infrageneric taxa. The lichen herbarium of the Botanical Garden of the University of Calabria (CLU) is the most relevant lichen collection from this region. It was established in 1985 and it presently includes 16926 specimens, most of which were collected in Calabria, although there are also several specimens from other parts of Italy and from abroad.
    New information: This dataset contains 16926 records of lichens for a total of 1316 species. Of the 15219 georeferenced specimens, 10254 were collected in Calabria, while 4965 in other administrative regions of Italy. The dataset is available through GBIF, as well as in ITALIC, the Information System of Italian Lichens.
    Language English
    Publishing date 2024-03-08
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.12.e116965
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A semi-automatic toolbox for markerless effective semantic feature extraction.

    Pastore, Vito Paolo / Moro, Matteo / Odone, Francesca

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 11899

    Abstract: VisionTool is an open-source python toolbox for semantic features extraction, capable to provide accurate features detectors for different applications, including motion analysis, markerless pose estimation, face recognition and biological cell tracking. ...

    Abstract VisionTool is an open-source python toolbox for semantic features extraction, capable to provide accurate features detectors for different applications, including motion analysis, markerless pose estimation, face recognition and biological cell tracking. VisionTool leverages transfer-learning with a large variety of deep neural networks allowing high-accuracy features detection with few training data. The toolbox offers a friendly graphical user interface, efficiently guiding the user through the entire process of features extraction. To facilitate broad usage and scientific community contribution, the code and a user guide are available at https://github.com/Malga-Vision/VisionTool.git .
    MeSH term(s) Cell Tracking ; Semantics ; Software
    Language English
    Publishing date 2022-07-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-16014-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.

    Menin, Silvia / Pavan, Matteo / Salmaso, Veronica / Sturlese, Mattia / Moro, Stefano

    International journal of molecular sciences

    2023  Volume 24, Issue 4

    Abstract: Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring ... ...

    Abstract Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refinement of docking results. TTMD evaluates the conservation of the native binding mode throughout a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints. The protocol was successfully applied to retrieve the native-like binding pose among a set of decoy poses of drug-like ligands generated on four different pharmaceutically relevant biological targets, including casein kinase 1δ, casein kinase 2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease.
    MeSH term(s) Humans ; COVID-19 ; Ligands ; Molecular Docking Simulation/methods ; Molecular Dynamics Simulation ; Protein Binding ; SARS-CoV-2/chemistry ; SARS-CoV-2/drug effects
    Chemical Substances Ligands
    Language English
    Publishing date 2023-02-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24043596
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.

    Pavan, Matteo / Bassani, Davide / Sturlese, Mattia / Moro, Stefano

    NAR genomics and bioinformatics

    2022  Volume 4, Issue 4, Page(s) lqac088

    Abstract: Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins to control the genome expression and several biological processes. Due to its characteristic structural features, this polymer can mold itself into different ... ...

    Abstract Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins to control the genome expression and several biological processes. Due to its characteristic structural features, this polymer can mold itself into different three-dimensional structures able to recognize target biomolecules with high affinity and specificity, thereby attracting the interest of drug developers and medicinal chemists. One successful example of the exploitation of RNA's structural and functional peculiarities is represented by aptamers, a class of therapeutic and diagnostic tools that can recognize and tightly bind several pharmaceutically relevant targets, ranging from small molecules to proteins, making use of the available structural and conformational freedom to maximize the complementarity with their interacting counterparts. In this scientific work, we present the first application of Supervised Molecular Dynamics (SuMD), an enhanced sampling Molecular Dynamics-based method for the study of receptor-ligand association processes in the nanoseconds timescale, to the study of recognition pathways between RNA aptamers and proteins, elucidating the main advantages and limitations of the technique while discussing its possible role in the rational design of RNA-based therapeutics.
    Language English
    Publishing date 2022-11-29
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqac088
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Sodium or Not Sodium: Should Its Presence Affect the Accuracy of Pose Prediction in Docking GPCR Antagonists?

    Bassani, Davide / Pavan, Matteo / Sturlese, Mattia / Moro, Stefano

    Pharmaceuticals (Basel, Switzerland)

    2022  Volume 15, Issue 3

    Abstract: The function of the allosteric sodium ion in stabilizing the inactive form of GPCRs has been extensively described in the past decades. Its presence has been reported to be essential for the binding of antagonist molecules in the orthosteric site of ... ...

    Abstract The function of the allosteric sodium ion in stabilizing the inactive form of GPCRs has been extensively described in the past decades. Its presence has been reported to be essential for the binding of antagonist molecules in the orthosteric site of these very important therapeutical targets. Among the GPCR-antagonist crystal structures available, in most cases, the sodium ion could not be experimentally resolved, obliging computational scientists using GPCRs as targets for virtual screening to ask: "Should the sodium ion affect the accuracy of pose prediction in docking GPCR antagonists?" In the present study, we examined the performance of three orthogonal docking programs in the self-docking of GPCR antagonists to try to answer this question. The results of the present work highlight that if the sodium ion is resolved in the crystal structure used as the target, it should also be taken into account during the docking calculations. If the crystallographic studies were not able to resolve the sodium ion then no advantage would be obtained if this is manually inserted in the virtual target. The outcomes of the present analysis are useful for researchers exploiting molecular docking-based virtual screening to efficiently identify novel GPCR antagonists.
    Language English
    Publishing date 2022-03-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph15030346
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?

    Pavan, Matteo / Bassani, Davide / Sturlese, Mattia / Moro, Stefano

    Journal of enzyme inhibition and medicinal chemistry

    2022  Volume 37, Issue 1, Page(s) 1077–1082

    Abstract: Despite a huge effort by the scientific community to determine the animal reservoir of SARS-CoV-2, which led to the identification of several SARS-CoV-2-related viruses both in bats and in pangolins, the origin of SARS-CoV-2 is still not clear. Recently, ...

    Abstract Despite a huge effort by the scientific community to determine the animal reservoir of SARS-CoV-2, which led to the identification of several SARS-CoV-2-related viruses both in bats and in pangolins, the origin of SARS-CoV-2 is still not clear. Recently, Temmam et al. reported the discovery of bat coronaviruses with a high degree of genome similarity with SARS-CoV-2, especially concerning the RBDs of the S protein, which mediates the capability of such viruses to enter and therefore infect human cells through a hACE2-dependent pathway. These viruses, especially the one named BANAL-236, showed a higher affinity for the hACE2 compared to the original strain of SARS-CoV-2. In the present work, we analyse the similarities and differences between the 3CL protease (main protease, M
    MeSH term(s) Animals ; Chiroptera/virology ; Coronavirus/enzymology ; Coronavirus 3C Proteases ; SARS-CoV-2
    Chemical Substances Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2022-04-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2082578-X
    ISSN 1475-6374 ; 1475-6366
    ISSN (online) 1475-6374
    ISSN 1475-6366
    DOI 10.1080/14756366.2022.2062336
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3004: Show issues Location:
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