Falanga AP, Lupia A, Tripodi L, Morgillo CM, Moraca F, Roviello GN, Catalanotti B, Amato J, Pastore L, Cerullo V, D'Errico S, Piccialli G, Oliviero G, Borbone N
Exploring the DNA2-PNA heterotriplex formation in targeting the Bcl-2 gene promoter: A structural insight by physico-chemical and microsecond-scale MD investigation
Heliyon, 2024 Jan 22; N/D: N/D-N/D.

Autiero I, Vitagliano L
Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers
Mol Ther Nucleic Acids (ISSN: 2162-2531linking), 2023 Dec 12; 34: 102039-102039.

Troisi R, Balasco N, Autiero I, Sica F, Vitagliano L
New insight into the traditional model of the coagulation cascade and its regulation: illustrated review of a three-dimensional view
Res Pract Thromb Haemost (ISSN: 2475-0379linking), 2023 Aug 7; 7 (6 ): 102160-102160.

Diaferia C, Rosa E, Balasco N, Sibillano T, Morelli G, Giannini C, Vitagliano L, Accardo A
The introduction of a cysteine residue modulates the mechanical properties of aromatic-based solid aggregates and self-supporting hydrogels
Chemistry (ISSN: 0947-6539linking, 1521-3765electronic), 2021 Oct 25; 27(60): 14886-14898.

Asha H, Green JA, Martinez-fernandez L, Esposito L, Improta R
Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2021 Aug 7; 26(16): N/D-N/D.

Sadremomtaz A, Al-dahmani ZM, Ruiz-moreno AJ, Monti A, Wang C, Azad T, Bell JC, Doti N, Velasco-velázquez MA, De Jong D, De Jonge J, Smit J, Dömling A, Van Goor H, Groves MR
Synthetic Peptides That Antagonize the Angiotensin-Converting Enzyme-2 (ACE-2) Interaction with SARS-CoV-2 Receptor Binding Spike Protein
J Med Chem (ISSN: 0022-2623linking, 0022-2623print), 2021 Jul 30; N/D: N/D-N/D.

Alterio V, Langella E, Buonanno M, Esposito D, Nocentini A, Berrino E, Bua S, Polentarutti M, Supuran CT, Monti SM, De Simone G
Zeta-carbonic anhydrases show CS(2) hydrolase activity: A new metabolic carbon acquisition pathway in diatoms?
Comput Struct Biotechnol J (ISSN: 2001-0370linking), 2021 Jun 5; 19: 3427-3436.

Mulliri S, Laaksonen A, Spanu P, Farris R, Farci M, Mingoia F, Roviello GN, Mocci F
Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1, 2-a]benzo[1, 2, 3, 4]tetrazine-3-one Derivatives with c-Myc G4-DNA
Int J Mol Sc (ISSN: 1422-0067linking, 1422-0067electronic, 1661-6596), 2021 Jun 2; 22(11): 6028-6028.

Farina B, Andrea C, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Paladino A, Acconcia C, Teresa Gentile M, Saviano M, Fattorusso R, Zaccaro L, Russo L
A novel approach for studying receptor-ligand interactions on living cells surface by using NUS/T1ρ-NMR methodologies combined with computational techniques: The RGDechi15D-α(v)β(5) integrin complex
Comput Struct Biotechnol J (ISSN: 2001-0370linking), 2021 May 29; 19: 3303-3318.

Troisi R, Balasco N, Vitagliano L, Sica F
Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites
J Biomol Struct Dyn (ISSN: 0739-1102linking, 1538-0254electronic), 2021 Apr; 39(6): 2199-2209.

Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A
Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information
Front Bioeng Biotechnol (ISSN: 2296-4185linking), 2021 Mar 3; 9: 641372-641372.

Marasco D, Vicidomini C, Krupa P, Cioffi F, Pham DQH, Li MS, Florio D, Broersen K, De Pandis MF, Roviello GN
Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine based compounds on β-amyloid aggregation
Chem Biol Interact (ISSN: 0009-2797linking), 2021 Jan 25; 334: 109300-109301.

Vincenzi M, Mercurio FA, Leone M
NMR spectroscopy in the conformational analysis of peptides: an overview
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2021; 28(14): 2729-2782.

Vincenzi M, Leone M
The fight against human viruses: how NMR can help
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2021; 28(22): 4380-4453.

Zhang P, Moretti M, Allione M, Tian Y, Ordonez-loza J, Altamura D, Giannini C, Torre B, Das G, Li E, Thoroddsen ST, Sarathy SM, Autiero I, Giugni A, Gentile F, Malara N, Marini M, Di Fabrizio E
A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth
Commun Biol (ISSN: 2399-3642linking), 2020 Aug 20; 3(1): 457-457.

Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R
A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping
Cells (ISSN: 2073-4409linking, 2073-4409electronic), 2020 May 20; 9(5): 1297-1297.

Moreira M, Ruggiero A, Esposito L, Choi HG, Kim HJ, Berisio R
Structural features of HtpGMtb and HtpG-ESAT6Mtb vaccine antigens against tuberculosis: Molecular determinants of antigenic synergy and cytotoxicity modulation
Int J Biol Macromol (ISSN: 0141-8130linking, 1879-0003electronic), 2020 May 4; 158: 305-317.

Vincenzi M, Mercurio FA, Leone M
Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2020; 27(37): 6306-6355.

Vincenzi M, Mercurio FA, Leone M
Sam Domains in Multiple Diseases
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2020; 27(3): 450-476.

Balasco N, Smaldone G, Vitagliano L
The Structural Versatility of the BTB Domains of KCTD Proteins and Their Recognition of the GABA(B) Receptor
Biomolecules (ISSN: 2218-273xlinking), 2019 Jul 31; 9 (8 ): N/D-N/D.

Banyasz A, Balanikas E, Martinez-fernandez L, Baldacchino G, Douki T, Improta R, Markovitsi D
Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features
J Phys Chem B (ISSN: 1520-5207linking, 1520-6106), 2019 Jun 13; 123(23): 4950-4957.

Ruggiero A, Smaldone G, Esposito L, Balasco N, Vitagliano L
Loop size optimization induces a strong thermal stabilization of the thioredoxin fold
Febs J (ISSN: 1742-464xlinking), 2019 May; 286(9): 1752-1764.

Diaferia C, Balasco N, Altamura D, Sibillano T, Gallo E, Roviello V, Giannini C, Morelli G, Vitagliano L, Accardo A
Assembly modes of hexaphenylalanine variants as function of the charge states of their terminal ends
Soft Matter (ISSN: 1744-683xlinking), 2018 Oct 17; 14 (40 ): 8219-8230.

Zambrano G, Ruggiero E, Malafronte A, Chino M, Maglio O, Pavone V, Nastri F, Lombardi A
Artificial Heme Enzymes for the Construction of Gold-Based Biomaterials
Int J Mol Sc (ISSN: 1422-0067electronic, 1422-0067linking, 1661-6596), 2018 Sep 24; 19(10): N/D-N/D.

Scollo F, Tempra C, Lolicato F, Sciacca MFM, Raudino A, Milardi D, La Rosa C
Phospholipids Critical Micellar Concentrations Trigger Different Mechanisms of Intrinsically Disordered Proteins Interaction with Model Membranes
J Phys Chem Lett (ISSN: 1948-7185electronic, 1948-7185linking), 2018 Sep 6; 9(17): 5125-5129.

Balasco N, Barone D, Iaccarino E, Sandomenico A, De Simone A, Ruvo M, Vitagliano L
Intrinsic structural versatility of the highly conserved 412-423 epitope of the Hepatitis C Virus E2 protein
Int J Biol Macromol (ISSN: 1879-0003electronic, 0141-8130linking), 2018 Sep; 116: 620-632.

Diaferia C, Balasco N, Sibillano T, Giannini C, Vitagliano L, Morelli G, Accardo A
Structural Characterization of Self-Assembled Tetra-Tryptophan Based Nanostructures: Variations on a Common Theme
Chemphyschem (ISSN: 1439-4235linking, 1439-7641), 2018 Jul 5; 19 (13 ): 1635-1642.

Autiero I, Ruvo M, Improta R, Vitagliano L
The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition
Bba-Gen Subjects (ISSN: 0304-4165print, 0304-4165linking, 1872-8006electronic), 2018 Apr; 1862(4): 1006-1016.

Martinez-fernandez L, Prampolini G, Cerezo J, Liu Y, Santoro F, Improta R
Solvent effect on the energetics of proton coupled electron transfer in guanine-cytosine pair in chloroform by mixed explicit and implicit solvation models
Chem Phys (ISSN: 0301-0104), 2018; 515: 493-501.

Balasco N, Barone D, Sandomenico A, Ruggiero A, Doti N, Berisio R, Ruvo M, Vitagliano L
Structural Versatility of Hepatitis C Virus Proteins: Implications for the Design of Novel Anti-HCV Intervention Strategies
Curr Med Chem (ISSN: 0929-8673, 1875-533x, 1875-533xelectronic), 2017 Nov 24; 24(36): 4081-4101.

Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R
Structure and dynamics of the multi-domain resuscitation promoting factor RpfB from Mycobacterium tuberculosis
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 2017 May; 35(6): 1322-1330.

Leiria Campo V, Riul TB, Oliveira Bortot L, Martins-teixeira MB, Fiori Marchiori M, Iaccarino E, Ruvo M, Dias-baruffi M, Carvalho I
A Synthetic MUC1 Glycopeptide Bearing betaGalNAc-Thr as a Tn Antigen Isomer Induces the Production of Antibodies against Tumor Cells
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-4227linking), 2017 Mar 16; 18(6): 527-538.

De Rosa L, Romanelli A, D'Andrea LD
Chemical ligation in Structural Biology in “Chemical Ligation: Tools for Biomolecules Synthesis and Modification”
John Wiley & Sons, 2017; N/D: N/D-N/D.

Lanza V, Travaglia A, Malgieri G, Fattorusso R, GrassoG, Di Natale G, Zito V, Arena G, Milardi D, Rizzarelli E
Ubiquitin Associates with the N-Terminal Domain of Nerve Growth Factor: The Role of Copper(II) Ions
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Dec 05; 22(49): 17767-17775.

Diaferia C, Sibillano T, Balasco N, Giannini C, Roviello V, Vitagliano L, Morelli G, Accardo A
Hierarchical Analysis of Self-Assembled PEGylated Hexaphenylalanine Photoluminescent Nanostructures
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Nov 7; 22(46): 16586-16597.

Nastri F, Chino M, Maglio O, Bhagi-damodaran A, Lu Y, Lombardi A
Design and engineering of artificial oxygen-activating metalloenzymes
Chem Soc Rev (ISSN: 0306-0012, 1460-4744), 2016 Sep 21; 45(18): 5020-5054.

Martinez-fernandez L, Pepino AJ, Segarra-marti J, Banyasz A, Garavelli M, Improta R
Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic, 1549-9618linking), 2016 Sep 13; 12(9): 4430-4439.

Langella E, Calce E, Saviano M, De Luca S
Structural identification of an HER2 receptor model binding pocket to optimize lead compounds: a combined experimental and computational approach
Mol Biosyst (ISSN: 1742-206x), 2016 Jun 21; 12(7): 2159-2167.

Banyasz A, Esposito L, Douki T, Perron M, Lepori C, Improta R, Markovitsi D
Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207linking), 2016 May 12; 120(18): 4232-4242.

Calvanese L, Falcigno L, D'Auria G
Essential Dynamics Analysis Captures the Concerted Motion of the Integrin-Binding Site in Jerdostatin, an RTS Disintegrin
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2015 Mar; 103(3): 158-166.

Balasco N, Barone D, Vitagliano L
Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 2015 Jan 12; 33(10): 2173-2179.

Vitiello G, Falanga A, Petruk AA, Merlino A, Fragneto G, Paduano L, Galdiero S, D'Errico G
Fusion of raft-like lipid bilayers operated by a membranotropic domain of the HSV-type I glycoprotein gH occurs through a cholesterol-dependent mechanism
Soft Matter (ISSN: 1744-683x), 2015; 11(15): 3003-3016.

Carbonniere P, Pouchan C, Improta R
Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: An ab initio molecular dynamics study
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2015; 17(17): 11615-11626.

Russo L, Palmieri M, Caso JV, Abrosca GD, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R
Towards understanding the molecular recognition process in prokaryotic zinc-finger domain
Eur J Med Chem (ISSN: 0223-5234, 1768-3254, 0223-5234linking), 2015; 91: 100-108.

Correale S, de Paola I, Morgillo CM, Federico A, Zaccaro L, Pallante P, Galeone A, Fusco A, Pedone E, Luque FJ, Catalanotti B
Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Nov 6; 9(11): e112082-e112082.

Pappalardo M, Shachaf N, Basile L, Milardi D, Zeidan M, Raiyn J, Guccione S, Rayan A
Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Oct 16; 9(10): e109340-e109340.

Petruk AA, Vergara A, Marasco D, Bikiel D, Doctorovich F, Estrin DA, Merlino A
Interaction between Proteins and Ir Based CO Releasing Molecules: Mechanism of Adduct Formation and CO Release
Inorg Chem (ISSN: 0020-1669, 1520-510x, 0020-1669linking), 2014 Oct 6; 53(19): 10456-10462.

Balasco N, Pirone L, Smaldone G, Di Gaetano S, Esposito L, Pedone E, Vitagliano L
Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations
Bba-Gen Subjects (ISSN: 0925-4439, 0006-3002, 1570-9639), 2014 Jul; 1844(7): 1289-1298.

Autiero I, Saviano M, Langella E
Molecular Dynamics Simulations Of Pna-Pna And Pna-Dna Duplexes By The Use Of New Parameters Implemented In The Gromacs Package: A Conformational And Dynamics Study
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2014 Feb 7; 16(5): 1868-1874.

Autiero I, Langella E, Saviano M
Insights Into The Mechanism Of Interaction Between Trehalose-Conjugated Beta-Sheet Breaker Peptides And Aβ(1-42) Fibrils By Molecular Dynamics Simulations
Mol Biosyst (ISSN: 1742-206x, 1742-2206, 1742-2051linking), 2013 Nov; 9(11): 2835-2841.

Petruk AA, Varriale S, Coscia MR, Mazzarella L, Merlino A, Oreste U
The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study
Bba-Gen Subjects (ISSN: 0005-2736, 0006-3002e, 0005-2736print), 2013 Nov; 1828(11): 2637-2645.

Alcides Petruk A, Vergara A, Estrin D, Merlino A
Molecular basis of the NO trans influence in quaternary T-state human hemoglobin: A computational study
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2013 Sep 2; 587(15): 2393-2398.

Paladino A, Zangi R
Ribose 2'-Hydroxyl Groups Stabilize RNA Hairpin Structures Containing GCUAA Pentaloop
J Chem Theory Comput (ISSN: 1549-9618linking), 2013 Feb 12; 9 (2 ): 1214-1221.

Vitiello G, Fragneto G, Petruk AA, Falanga A, Galdiero S, D'Ursi A, Merlino A, D'Errico G
Cholesterol modulates the fusogenic activity of a membranotropic domain of the FIV glycoprotein gp36
Soft Matter (ISSN: 1744-683x), 2013; 9(28): 6442-6456.

Caruso P, Causà M, Cimino P, Crescenzi O, D'Amore M, Improta R, Pavone M, Rega N
Effects of molecular dynamics and solvation on the electronic structure of molecular probes
Theor Chem Acc (ISSN: 1432-881x), 2012 Apr; 131(4): 1211-1212.

Merlino A, Vitiello G, Grimaldi M, Sica F, Busi E, Basosi R, D’Ursi A, Fragneto G, Paduano L, D’Errico G
Destabilization of Lipid Membranes by a Peptide Derived from Glycoprotein gp36 of Feline Immunodeficiency Virus: A Combined Molecular Dynamics/Experimental Study
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2012 Jan 12; 116(1): 401-412.

Boechi L, Marti MA, Vergara A, Sica F, Mazzarella L, Estrin DA, Merlino A
Protonation of Histidine 55 Affects the Oxygen Access to Heme in the Alpha Chain of the Hemoglobin from the Antarctic Fish Trematomus bernacchii
Iubmb Life (ISSN: 1521-6543, 1521-6551), 2011 Mar; 63(3): 175-182.

Milardi D, Sciacca MFM, Pappalardo M, Grasso DM, La Rosa C
The Role Of Aromatic Side-Chains In Amyloid Growth And Membrane Interaction Of The Islet Amyloid Polypeptide Fragment Lanflvh
Eur Biophys J, 2011 Jan; 40(1): 1-12.

Varriale S, Merlino A, Coscia MR, Mazzarella L, Oreste U
An evolutionary conserved motif is responsible for Immunoglobulin heavy chain packing in the B cell membrane
Molecular Phylogenetics And Evolution (ISSN: 1055-7903), 2010 Dec; 57(3): 1238-1244.

D'Auria G, Esposito C, Falcigno L, Calvanese L, Iaccarino E, Ruggiero A, Pedone C, Pedone E, Berisio R
Dynamical properties of cold shock protein A from Mycobacterium tuberculosis
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2010 Nov 26; 402(4): 693-698.

Paladino A, Colonna G, Facchiano AM, Costantini S
Functional hypothesis on miraculin' sweetness by a molecular dynamics approach
Biochem Biophys Res Commun (ISSN: 0006-291xlinking), 2010 Jun 4; 396 (3 ): 726-730.

Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L
Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2010 May 27; 114(20): 7002-7008.

Diana D, Ziaco B, Scarabelli G, Pedone C, Colombo G, D'Andrea LD, Fattorusso R
Structural analysis of a helical peptide unfolding pathway
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2010 May 10; 16(18): 5400-5407.

Vitagliano L, Stanzione F, De Simone A, Esposito L
Dynamics and Stability of Amyloid-Like Steric Zipper Assemblies with Hydrophobic Dry Interfaces
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1161-1171.

Pietropaolo A, Muccioli L, Zannoni C, Rizzarelli E
Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals
Chemphyschem (ISSN: 1439-7641, 1439-4235, 1439-7641electronic), 2009 Jul 13; 10(9-10): 1500-1510.

Vitagliano L, Esposito L, Pedone C, De Simone A
Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association
Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Dec 26; 377(4): 1036-1041.

De Simone A, Vitagliano L, Berisio R
Role of hydration in collagen triple helix stabilization
Biochem Biophys Res Commun (ISSN: 0006-291x), 2008 Jul 18; 372(1): 121-125.

Esposito L, Paladino A, Pedone C, Vitagliano L
Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations
Biophys J (ISSN: 1542-0086, 0006-3495, 0006-3495linking), 2008 May 15; 94(10): 4031-4040.

Improta R, Berisio R, Vitagliano L
Contribution of dipole-dipole interactions to the stability of the collagen triple helix
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2008 May; 17(5): 955-961.

Paladino A, Costantini S, Colonna G, Facchiano AM
Molecular modelling of miraculin: Structural analyses and functional hypotheses
Biochem Biophys Res Commun (ISSN: 0006-291xlinking), 2008 Feb 29; 367 (1 ): 26-32.

Vergara A, Merlino A, Pizzo E, D'Alessio G, Mazzarella L
A novel method for detection of selenomethionine incorporation in protein crystals via Raman microscopy
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2008 Feb; 64: 167-171.

Staiano M, Saviano M, Herman P, Grycznyski Z, Fini C, Varriale A, Parracino A, Kold AB, Rossi M, D'Auria S
Time-resolved fluorescence spectroscopy and molecular dynamics simulations point out the effects of pressure on the stability and dynamics of the porcine odorant-binding protein
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2008; 89(4): 284-291.

Vitale RM, Pedone C, Amodeo P, Antel J, Wurl M, Scozzafava A, Supuran CT, De Simone G
Molecular modeling study for the binding of zonisamide and topiramate to the human mitochondrial carbonic anhydrase isoform VA
Bioorg Med Chem (ISSN: 0968-0896, 1464-3391, 1464-3391electronic), 2007 Jun 15; 15(12): 4152-4158.

Ronga L, Langella E, Palladino P, Marasco D, Tizzano B, Saviano M, Pedone C, Improta R, Ruvo M
Does Tetracycline Bind Helix 2 Of Prion? An Integrated Spectroscopical And Computational Study Of The Interaction Between The Antibiotic And Alpha Helix 2 Human Prion Protein Fragments
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Feb 15; 66(3): 707-715.

Pappalardo M, Milardi D, Grasso D, La Rosa C
Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species
New J Chem (ISSN: 1144-0546), 2007; 31(6): 901-905.

Esposito L, Pedone C, Vitagliano L
Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation
P Natl Acad Sci Usa (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2006 Sep 1; 103(31): 11533-11538.

Langella E, Improta R, Crescenzi O, Barone V
Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.

Merlino A, Esposito L, Vitagliano L
Polyglutamine Repeats And Beta-Helix Structure: Molecular Dynamics Study
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jun 1; 63(4): 918-927.

De Simone A, Dodson GG, Fraternali F, Zagari A
Water molecules as structural determinants among prions of low sequence identity
Febs Lett (ISSN: 0014-5793print, 0014-5793linking, 1873-3468electronic), 2006 May 1; 580(10): 2488-2494.

De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.

Esposito L, Daggett V
Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2005 Mar 8; 44(9): 3358-3368.

Merlino A, Ceruso MA, Vitagliano L, Mazzarella L
Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2005 Mar; 88(3): 2003-2012.

Vergara A, Lorber B, Sauter C, Giege R, Zagari A
Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology
Biophys Chem (ISSN: 0301-4622, 0301-4622linking), 2005; 118(2-3): 102-112.

Langella E, Improta R, Barone V
Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.

Vitale RM, Pedone C, De Benedetti PG, Fanelli F
Structural features of the inactive and active states of the melanin-concentrating hormone receptors: Insights from molecular simulations
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2004 Sep 15; 56(3): 430-448.

Merlino A, Vitagliano L, Ceruso MA, Mazzarella L
Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2003 Oct 1; 53(1): 101-110.

Oliva R, Falcigno L, D'Auria G, Dettin M, Scarinci C, Pasquato A, Di Bello C, Paolillo L
Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2003 Sep 4; 4(8): 727-733.

Pappalardo M, Milardi D, Grasso DM, La Rosa C
Free energy perturbation and molecular dynamics calculations of copper binding to azurin
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2003 Apr 30; 24(6): 779-785.

Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
Global and local motions in ribonuclease A: A molecular dynamics study
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.

Oliva R, Leone M, Falcigno L, D'Auria G, Dettin M, Scarinci C, Di Bello C, Paolillo L
Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2002 Mar 15; 8(6): 1467-1473.

Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites
Eur J Biochem (ISSN: 0014-2956, 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.

Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites
Eur J Biochem (ISSN: 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.

D'Andrea LD, Mazzeo M, Isernia C, Rossi F, Saviano M, Gallo P, Paolillo L, Pedone C
Solution conformational preferences of a peptidic analogue of a natural macrolide
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1997; 42(3): 349-361.

Saviano M, Rossi F, Pavone V, Di Blasio B, Pedone C
Molecular dynamics simulation in vacuo and in solution of [Aib5, 6-D- Ala8] Cyclolinopeptide A: A conformational and comparative study
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 1992 Jun; 9(6): 1045-1060.