Publications

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2018

Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection

Ballante, Flavio

Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection Book Chapter

Mavromoustakos, Thomas; Kellici, Tahsin F (Ed.): 1824 , Chapter 5, pp. 67-88, Springer Nature, 2018, ISBN: 978-1-4939-8630-9.

Links | BibTeX | Tags: Docking Assessment, Molecular Docking, Molecular Modeling

2017

Structural Insights of SmKDAC8 Inhibitors: Targeting Schistosoma Epigenetics Through a Combined Structure-Based 3D QSAR, in vitro and Synthesis Strategy

Ballante, Flavio; Reddy, Rajasekhar D; Zhou, Nancy J; Marshall, Garland R

Structural Insights of SmKDAC8 Inhibitors: Targeting Schistosoma Epigenetics Through a Combined Structure-Based 3D QSAR, in vitro and Synthesis Strategy Journal Article

Bioorganic & Medicinal Chemistry, 2017.

Links | BibTeX | Tags: 3D QSAR, Biochemistry, COMBINEr, Molecular Docking, Molecular Modeling, Organic Chemistry, PLS, Schistosoma mansoni, Virtual Screening

2016

Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors

Reddy, Rajasekhar D; Ballante, Flavio; Zhou, Nancy J; Marshall, Garland R

Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors Journal Article

European Journal of Medicinal Chemistry, 127 , pp. Pages 531–553, 2016.

Abstract | Links | BibTeX | Tags: Biochemistry, HDAC, Molecular Docking

2015

An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design

Flavio, Ballante ; Garland R, Marshall

An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design Journal Article

Journal of Chemical Information and Modeling, 56 (1), pp. 54-72, 2015.

Abstract | Links | BibTeX | Tags: Chemoinformatics, Clusterizer, DockAccessor, Docking Assessment, Molecular Docking, Molecular Modeling

Design and Synthesis of Simplified Largazole Analogs as Isoform-Selective Human Lysine Deacetylase Inhibitors

Damodara, Reddy Nandarapu; Flavio, Ballante; Timothy, Chuang; Adele, Pirolli; Biagina, Marrocco; Garland R, Marshall

Design and Synthesis of Simplified Largazole Analogs as Isoform-Selective Human Lysine Deacetylase Inhibitors Journal Article

Journal of Medicinal Chemistry, in press , 2015.

Abstract | Links | BibTeX | Tags: Biochemistry, HDAC, Molecular Docking, Organic Chemistry

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand-and structure-based approaches

Rino, Ragno; Flavio, Ballante; Adele, Pirolli; Richard B, Wickersham III ; Alexandros, Patsilinakos; Stéphanie, Hesse; Enrico, Perspicace; Gilbert, Kirsch

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand-and structure-based approaches Journal Article

Journal of Computer-Aided Molecular Design, 29 (8), pp. 757-776, 2015.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Ligand-Based Design, Molecular Docking, Molecular Modeling, Pharmacophoric Model, PLS, VEGFR-2

2014

Exploring the Role of 2 ‑ Chloro-6- fluoro Substitution in 2 ‑ Alkylthio-6- benzyl-5-alkylpyrimidin-4(3 H ) ‑ ones: Effects in HIV-1-Infected Cells and in HIV ‑ 1 Reverse Transcriptase Enzymes

Dante, Rotili; Domenico, Tarantino; Maxim B, Nawrozkij ; Alexandre S, Babushkin ; Giorgia, Botta; Biagina, Marrocco; Roberto, Cirilli; Sergio, Menta; Roger, Badia; Emmanuele, Crespan; Flavio, Ballante; Rino, Ragno; José A, Esté ; Giovanni, Maga; Antonello, Mai

Exploring the Role of 2 ‑ Chloro-6- fluoro Substitution in 2 ‑ Alkylthio-6- benzyl-5-alkylpyrimidin-4(3 H ) ‑ ones: Effects in HIV-1-Infected Cells and in HIV ‑ 1 Reverse Transcriptase Enzymes Journal Article

Journal of Medicinal Chemistry, 57 (12), pp. 5212-5225, 2014.

Abstract | Links | BibTeX | Tags: Biochemistry, COMBINEr, DABO, HIV-1, HIV-RT, Molecular Docking, Molecular Modeling, NNRTIs, Organic Chemistry, PLS

Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application

Antonia, Caroli; Flavio, Ballante; Richard B, Wickersham III ; Federico, Corelli; Rino, Ragno

Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application Journal Article

Journal of Chemical Information and Modeling, 54 (3), pp. 970-977, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, HSP90, Ligand-Based Design, Molecular Docking, Molecular Modeling, MPGRS, Pharmacophoric Model, PLS, Virtual Screening

Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening

Flavio, Ballante; Antonia, Caroli; Richard B, Wickersham III ; Rino, Ragno

Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening Journal Article

Journal of Chemical Information and Modeling, 54 (3), pp. 956-969, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, HSP90, Ligand-Based Design, Molecular Docking, Pharmacophoric Model, PLS, Virtual Screening

Flavio, Ballante

Application of Medicinal Chemistry Methods on Different Classes of Drugs PhD Thesis

Sapienza University of Rome, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Biochemistry, BSAO, Chemoinformatics, Chemometrics, COMBINEr, CoMFA, DABO, DockAccessor, Docking Assessment, HCV NS5B, HDAC, HIV-1, HIV-RT, HSP90, HUVEC, Ligand-Based Design, Molecular Docking, Molecular Modeling, MPGRS, NNRTIs, Opioid-Receptor Antagonists, Organic Chemistry, Pharmacophoric Model, PLS, Tuberculosis, VEGFR-2, Virtual Screening

2013

Computational strategies to design new highly potential BSAO polyamine substrates - Abstracts presented at the 13th International Congress on Amino acids, peptides and proteins

Flavio, Ballante; Giampiero, Tempera; Enzo, Agostinelli; Rino, Ragno

Computational strategies to design new highly potential BSAO polyamine substrates - Abstracts presented at the 13th International Congress on Amino acids, peptides and proteins Proceeding

Amino Acids, 45 (3), 2013.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Biochemistry, BSAO, Molecular Docking, Molecular Modeling, MPGRS

2012

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction

Laura, Silvestri; Flavio, Ballante; Antonello, Mai; Garland R, Marshall ; Rino, Ragno

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction Journal Article

Journal of Chemical Information and Modeling, 52 (8), pp. 2215-2235, 2012.

Abstract | Links | BibTeX | Tags: 3D QSAR, COMBINEr, HDAC, Molecular Docking, Molecular Modeling, PLS

2-(Alkyl/aryl) amino-6-benzylpyrimidin-4 (3H)-ones as inhibitors of wild-type and mutant HIV-1: enantioselectivity studies

Dante, Rotili; Alberta, Samuele; Domenico, Tarantino; Rino, Ragno; Ira, Musmuca; Flavio, Ballante; Giorgia, Botta; Ludovica, Morera; Marco, Pierini; Roberto, Cirilli; Maxim B, Nawrozkij ; Emmanuel, Gonzalez; Bonaventura, Clotet; Marino, Artico; José A, Esté ; Giovanni, Maga; Antonello, Mai

2-(Alkyl/aryl) amino-6-benzylpyrimidin-4 (3H)-ones as inhibitors of wild-type and mutant HIV-1: enantioselectivity studies Journal Article

Journal of Medicinal Chemistry, 55 (7), pp. 3558-3562, 2012.

Abstract | Links | BibTeX | Tags: Biochemistry, COMBINEr, DABO, HIV-1, Molecular Docking, Molecular Modeling, NNRTIs, Organic Chemistry