2020

• Calonaci N., Jones A., Cuturello F., Sattler M., Bussi G.
  Machine learning a model for RNA structure prediction
  NAR GENOMICS AND BIOINFORMATICS, 2 (4) (2020)
  doi:
• Allegra M., Facco E., Denti F., Laio A., Mira A.
  Data segmentation based on the local intrinsic dimension
  SCIENTIFIC REPORTS, 10 (1) (2020)
  doi:
• Frohlking T., Bernetti M., Calonaci N., Bussi G.
  Toward empirical force fields that match experimental observables
  JOURNAL OF CHEMICAL PHYSICS, 152 (23) (2020)
  doi:
• Suma A., Coronel L., Bussi G., Micheletti C.
  Directional translocation resistance of Zika xrRNA
  NATURE COMMUNICATIONS, 11 (1) (2020)
  doi:
• Spinello A., Saltalamacchia A., Magistrato A.
  Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations
  JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 11 (12) pp.4785-4790 (2020)
  doi:
• Saltalamacchia A., Casalino L., Borisek J., Batista V., Rivalta I., Magistrato A.
  Decrypting the Information Exchange Pathways across the Spliceosome Machinery
  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 142 (18) pp.8403-8411 (2020)
  doi:
• Cuturello F., Tiana G., Bussi G.
  Assessing the accuracy of direct-coupling analysis for RNA contact prediction
  RNA, 26 (5) pp.637-647 (2020)
  doi:
• Ritacco I., Saltalamacchia A., Spinello A., Ippoliti E., Magistrato A.
  All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s
  JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 11 (4) pp.1189-1193 (2020)
  doi:
• Sormani G., Rodriguez A., Laio A.
  Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its C-alpha Carbons
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 16 (1) pp.80-87 (2020)
  doi:

2019

• Rizzato F., Zamuner S., Pagnani A., Laio A.
  A common root for coevolution and substitution rate variability in protein sequence evolution
  SCIENTIFIC REPORTS, 9 (2019)
  doi:
• Rosa A., Di Stefano M., Micheletti C.
  Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes
  FRONTIERS IN MOLECULAR BIOSCIENCES, 6 (2019)
  doi:
• Suma A., Poppleton E., Matthies M., Sulc P., Romano F., Louis A., Doye J., Micheletti C., Rovigatti L.
  TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
  JOURNAL OF COMPUTATIONAL CHEMISTRY, 40 (29) pp.2586-2595 (2019)
  doi:
• Valdes A., Coronel L., Martinez-Garcia B., Segura J., Dyson S., Diaz-Ingelmo O., Micheletti C., Roca J.
  Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA
  NUCLEIC ACIDS RESEARCH, 47 (13) pp.6946-6955 (2019)
  doi:
• Weiss L., Marenda M., Micheletti C., Likos C.
  Hydrodynamics and Filtering of Knotted Ring Polymers in Nanochannels
  MACROMOLECULES, 52 (11) pp.4111-4119 (2019)
  doi:
• Cesari A., Bottaro S., Lindorfr-Larsen K., Banas P., Sponer J., Bussi G.
  Fitting Corrections to an RNA Force Field Using Experimental Data
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 15 (6) pp.3425-3431 (2019)
  doi:
• Bonomi M., Bussi G., Camilloni C., Tribello G., Banas P., Barducci A., Bernetti M., Bolhuis P., Bottaro S., Branduardi D., Capelli R., Carloni P., Ceriotti M., Cesari A., Chen H., Chen W., Colizzi F., De S., De La Pierre M., Donadio D., Drobot V., Ensing B., Ferguson A., Filizola M., Fraser J., Fu H., Gasparotto P., Gervasio F., Giberti F., Gil-Ley A., Giorgino T., Heller G., Hocky G., Iannuzzi M., Invernizzi M., Jelfs K., Jussupow A., Kirilin E., Laio A., Limongelli V., Lindorff-Larsen K., Lohr T., Marinelli F., Martin-Samos L., Masetti M., Meyer R., Michaelides A., Molteni C., Morishita T., Nava M., Paissoni C., Papaleo E., Parrinello M., Pfaendtner J., Piaggi P., Piccini G., Pietropaolo A., Pietrucci F., Pipolo S., Provasi D., Quigley D., Raiteri P., Raniolo S., Rydzewski J., Salvalaglio M., Sosso G., Spiwok V., Sponer J., Swenson D., Tiwary P., Valsson O., Vendruscolo M., Voth G., White A.
  Promoting transparency and reproducibility in enhanced molecular simulations
  NATURE METHODS, 16 (8) pp.670-673 (2019)
  doi:
• Pinamonti G., Paul F., Noe F., Rodriguez A., Bussi G.
  The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
  JOURNAL OF CHEMICAL PHYSICS, 150 (15) (2019)
  doi:
• Marchetti F., Capelli R., Rizzato F., Laio A., Colombo G.
  The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions
  JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10 (7) pp.1489-1497 (2019)
  doi:
• Sgrignani J., Casalino L., Doro F., Spinello A., Magistrato A.
  Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery?
  FUTURE MEDICINAL CHEMISTRY, 11 (7) pp.771-792 (2019)
  doi:
• Amici G., Caraglio M., Orlandini E., Micheletti C.
  Topologically Linked Chains in Confinement
  ACS MACRO LETTERS, 8 (4) pp.442-446 (2019)
  doi:
• Facco E., Pagnani A., Russo E., Laio A.
  The intrinsic dimension of protein sequence evolution
  PLOS COMPUTATIONAL BIOLOGY, 15 (4) (2019)
  doi:
• Coronel L., Suma A., Micheletti C.
  Dynamics of Supercoiled Knotted DNA: Large Scale Rearrangements and Persistent Multi Strand Interlocking
  BIOPHYSICAL JOURNAL, 116 (3) (2019)
  doi:
• Galvanetto N., Ilieva N., Laio A., Torre V.
  Clustering and Identification of Force Spectra from Native Membranes
  BIOPHYSICAL JOURNAL, 116 (3) (2019)
  doi:
• Bottaro S., Bussi G., Pinamonti G., Reisser S., Boomsma W., Lindorff-Larsen K.
  Barnaba: software for analysis of nucleic acid structures and trajectories
  RNA, 25 (2) pp.219-231 (2019)
  doi:
• Uehara E., Coronel L., Micheletti C., Deguchi T.
  Bimodality in the knotting probability of semiflexible rings suggested by mapping with self-avoiding polygons
  REACTIVE & FUNCTIONAL POLYMERS, 134 pp.141-149 (2019)
  doi:

• Papale A., Rosa A.
  The Ising model in swollen vs. compact polymers: Mean-field approach and computer simulations
  EUROPEAN PHYSICAL JOURNAL E, 41 (12) (2018)
  doi:
• Rangan R., Bonomi M., Heller G., Cesari A., Bussi G., Vendruscolo M.
  Determination of Structural Ensembles of Proteins: Restraining vs Reweighting
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (12) pp. 6632-6641 (2018)
  doi:
• Franzini S., Reatto L., Pini D.
  Formation of cluster crystals in an ultra-soft potential model on a spherical surface
  SOFT MATTER, 14 (43) pp. 8724-8739 (2018)
  doi:
• Spinello A., Cusimano M., Schillaci D., Inguglia L., Barone G., Arizza V.
  Antimicrobial and Antibiofilm Activity of a Recombinant Fragment of -Thymosin of Sea Urchin Paracentrotus lividus
  MARINE DRUGS, 16 (10) (2018)
  doi:
• Pezzotta A., Adorisio M., Celani A.
  Chemotaxis emerges as the optimal solution to cooperative search games
  PHYSICAL REVIEW E, 98 (4) (2018)
  doi:
• Coronel L., Suma A., Micheletti C.
  Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking
  NUCLEIC ACIDS RESEARCH, 46 (15) pp. 7533-7541 (2018)
  doi:
• Marenda M., Orlandini E., Micheletti C.
  Discovering privileged topologies of molecular knots with self-assembling models
  NATURE COMMUNICATIONS, 9 (2018)
  doi:
• Spinello A., Pavlin M., Casalino L., Magistrato A.
  A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme?
  CHEMISTRY-A EUROPEAN JOURNAL, 24 (42) pp. 10840-10849 (2018)
  doi:
• Suma A., Di Stefano M., Micheletti C.
  Electric-Field-Driven Trapping of Polyelectrolytes in Needle-like Backfolded States
  MACROMOLECULES, 51 (12) pp. 4462-4470 (2018)
  doi:
• Casalino L., Palermo G., Spinello A., Rothlisberger U., Magistrato A.
  All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115 (26) pp. 6584-6589 (2018)
  doi:
• Nahali N., Rosa A.
  Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains
  JOURNAL OF CHEMICAL PHYSICS, 148 (19) (2018)
  doi:
• Cesari A., Reisser S., Bussi G.
  Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments
  COMPUTATION, 6 (1) (2018)
  doi:
• Rodriguez A., d'Errico M., Facco E., Laio A.
  Computing the Free Energy without Collective Variables
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (3) pp. 1206-1215 (2018)
  doi:
• Cesari A., Bottaro S., Bussi G.
  Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages
  BIOPHYSICAL JOURNAL, 114 (3) (2018)
  doi:
• Adorisio M., Pezzotta A., de Mulatier C., Micheletti C., Celani A.
  Exact and Efficient Sampling of Conditioned Walks
  JOURNAL OF STATISTICAL PHYSICS, 170 (1) pp. 79-100 (2018)
  doi:

2017

• Cugliandolo L., Digregorio P., Gonnella G., Suma A.
  Phase Coexistence in Two-Dimensional Passive and Active Dumbbell Systems
  PHYSICAL REVIEW LETTERS, 119 (26) (2017)
  doi:
• Granata D., Ponzoni L., Micheletti C., Carnevale V.
  Patterns of coevolving amino acids unveil structural and dynamical domains
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (50) (2017)
  doi:
• Giuntoli A., Calonaci N., Bernini S., Leporini D.
  Effect of Nematic Ordering on the Elasticity and Yielding in Disordered Polymeric Solids
  JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 55 (23) pp. 1760-1769 (2017)
  doi:
• Michieletto D., Nahali N., Rosa A.
  Glassiness and Heterogeneous Dynamics in Dense Solutions of Ring Polymers
  PHYSICAL REVIEW LETTERS, 119 (19) (2017)
  doi:
• Cagnetta F., Corberi F., Gonnella G., Suma A.
  Large Fluctuations and Dynamic Phase Transition in a System of Self-Propelled Particles
  PHYSICAL REVIEW LETTERS, 119 (15) (2017)
  doi:
• Rizzato F., Rodriguez A., Biarnes X., Laio A.
  Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms
  GENETICS, 207 (2) pp. 643-652 (2017)
  doi:
• Facco E., d'Errico M., Rodriguez A., Laio A.
  Estimating the intrinsic dimension of datasets by a minimal neighborhood information
  SCIENTIFIC REPORTS, 7 (2017)
  doi:
• Maity S., Ilieva N., Laio A., Torre V., Mazzolini M.
  New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods
  SCIENTIFIC REPORTS, 7 (2017)
  doi:
• Coronel L., Orlandini E., Micheletti C.
  Non-monotonic knotting probability and knot length of semiflexible rings: the competing roles of entropy and bending energy
  SOFT MATTER, 13 (23) pp. 4260-4267 (2017)
  doi:
• Cunha R., Bussi G.
  Unraveling Mg2+-RNA binding with atomistic molecular dynamics
  RNA, 23 (5) pp. 628-638 (2017)
  doi:
• Suma A., Micheletti C.
  Pore translocation of knotted DNA rings
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (15) (2017)
  doi:
• Orlandini E., Polles G., Marenduzzo D., Micheletti C.
  Self-assembly of knots and links
  JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, (2017)
  doi:
• Grilli J., Adorisio M., Suweis S., Barabas G., Banavar J., Allesina S., Maritan A.
  Feasibility and coexistence of large ecological communities
  NATURE COMMUNICATIONS, 8 (2017)
  doi:
• Suma A., Micheletti C.
  Pore Translocation of DNA Chains with Physical Knots
  BIOPHYSICAL JOURNAL, 112 (3) (2017)
  doi:
• Jackson S., Suma A., Micheletti C.
  How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
  CURRENT OPINION IN STRUCTURAL BIOLOGY, 42 pp. 6-14 (2017)
  doi:
• Pinamonti G., Zhao J., Condon D., Paul F., Noe F., Turner D., Bussi G.
  Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13 (2) pp. 926-934 (2017)
  doi:
• Pezzotta A., Adorisio M., Celani A.
  From conformational spread to allosteric and cooperative models of E. coli flagellar motor
  JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, (2017)
  doi:
• Ponzoni L., Rossetti G., Maggi L., Giorgetti A., Carloni P., Micheletti C.
  Unifying view of mechanical and functional hotspots across class A GPCRs
  PLOS COMPUTATIONAL BIOLOGY, 13 (2) (2017)
  doi:
• Marenda M., Orlandini E., Micheletti C.
  Sorting ring polymers by knot type with modulated nanochannels
  SOFT MATTER, 13 (4) pp. 795-802 (2017)
  doi:
• Soler M., Rodriguez A., Russo A., Adedeji A., Foumthuim C., Cantarutti C., Ambrosetti E., Casalis L., Corazza A., Scoles G., Marasco D., Laio A., Fortuna S.
  Computational design of cyclic peptides for the customized oriented immobilization of globular proteins
  PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19 (4) pp. 2740-2748 (2017)
  doi:
• Casalino L., Palermo G., Abdurakhmonova N., Rothlisberger U., Magistrato A.
  Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13 (1) pp. 340-352 (2017)
  doi:

2016

• Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries
  Marenda M., Zanardo M., Trovato A., Seno F., Squartini A.
  SCIENTIFIC REPORTS Volume: 6 2016
  
• Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
  Cesari A., Gil-Ley A., Bussi G.
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 12 Issue: 12 Pages 6192-6200 2016
  
• Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations
  Casalino L., Magistrato A.
  INORGANICA CHIMICA ACTA Volume: 452 Pages 73-81 2016
  
• Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
  Sarti E., Gladich I., Zamuner S., Correia B., Laio A.
  PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Volume: 84 Issue: 9 Pages 1312-1320 2016
  
• Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
  Casalino L., Palermo G., Rothlisberger U., Magistrato A.
  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 138 Issue: 33 Pages 10374-10377 2016
  
• Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement
  Polles G., Odandini E., Micheletti C.
  ACS MACRO LETTERS Volume: 5 Issue: 8 Pages 931-935 2016
  
• RNA folding pathways in stop motion
  Bottaro S., Gil-Ley A., Bussi G.
  NUCLEIC ACIDS RESEARCH Volume: 44 Issue: 12 Pages 5883-5891 2016
  
• Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
  Rizzato F., Rodriguez A., Laio A.
  BMC BIOINFORMATICS Volume: 17 2016
  
• Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
  Gil-Ley A., Bottaro S., Bussi G.
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 12 Issue: 6 Pages 2790-2798 2016
  
• Tracer motion in an active dumbbell fluid
  Suma A., Cugliandolo L., Gonnella G.
  JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2016
  
• Density effects in entangled solutions of linear and ring polymers
  Nahali N., Rosa A.
  JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 28 Issue: 6 2016
  

2015

• Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity
  Suma A., Rosa A., Micheletti C.
  ACS MACRO LETTERS Volume: 4 Issue: 12 Pages 1420-1424 2015
  
• Fluctuations of rotational and translational degrees of freedom in an interacting active dumbbell system
  Cugliandolo L., Gonnella G., Suma A.
  CHAOS SOLITONS & FRACTALS Volume: 81 Pages 556-566 2015
  
• ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
  Perez-Villa A., Darvas M., Bussi G.
  NUCLEIC ACIDS RESEARCH Volume: 43 Issue: 18 Pages 8725-34 2015
  
• Knotting dynamics of DNA chains of different length confined in nanochannels.
  Suma A., Orlandini E., Micheletti C.
  JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL Volume: 27 Issue: 35 Pages 354102-354102 2015
  
• Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
  Pinamonti G., Bottaro S., Micheletti C., Bussi G.
  NUCLEIC ACIDS RESEARCH Volume: 43 Issue: 15 Pages 7260-7269 2015
  
• SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets
  Ponzoni L., Polles G., Carnevale V., Micheletti C.
  STRUCTURE Volume: 23 Issue: 8 Pages 1516-1525 2015
  
• Motility-induced phase separation and coarsening in active matter
  Gonnella G., Marenduzzo D., Suma A., Tiribocchi A.
  COMPTES RENDUS PHYSIQUE Volume: 16 Issue: 3 Pages 316-331 2015
  
• Rotational and translational diffusion in an interacting active dumbbell system
  Cugliandolo L. F., Gonnella G., Suma A.
  PHYSICAL REVIEW E Volume: 91 Issue: 6 2015
  
• Native fold and docking pose discrimination by the same residue-based scoring function
  Sarti E., Granata D., Seno F., Trovato A., Laio A.
  PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Volume: 83 Issue: 4 Pages 621-630 2015
  
• Self-assembling knots of controlled topology by designing the geometry of patchy templates
  Polles G., Marenduzzo D., Orlandini E., Micheletti C.
  NATURE COMMUNICATIONS Volume: 6 2015
  
• Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
  Gil-Ley A., Bussi G.
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 3 Pages 1077-1085 2015
  
• Absence of knots in known RNA structures
  Micheletti C., Di Stefano M., Orland H.
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 112 Issue: 7 Pages 2052-2057 2015
  
• Using reweighted pulling simulations to characterize conformational changes in riboswitches.
  Di Palma F., Colizzi F., Bussi G.
  METHODS IN ENZYMOLOGY Volume: 553 Pages 139-62 2015
  
• Accurate Multiple Time Step in Biased Molecular Simulations
  Ferrarotti M. J., Bottaro S., Perez-Villa A., Bussi G.
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 1 Pages 139-146 2015
  

2014

• Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
  Bisha I., Rodriguez A., Laio A., Magistrato A.
  PLOS COMPUTATIONAL BIOLOGY Volume: 10 Issue: 12 2014
  
• The role of nucleobase interactions in RNA structure and dynamics
  Bottaro S., Di Palma F., Bussi G.
  NUCLEIC ACIDS RESEARCH Volume: 42 Issue: 21 Pages 13306-13314 2014
  
• Dynamics of a homogeneous active dumbbell system
  Suma A., Gonnella G., Laghezza G., Lamura A., Mossa A., Cugliandolo L. F.
  PHYSICAL REVIEW E Volume: 90 Issue: 5 2014
  
• Ru[(bpy)(2)(dppz)](2+) and Rh[(bpy)(2)(chrysi)](3+) Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation
  Franco D., Vargiu A. V., Magistrato A.
  INORGANIC CHEMISTRY Volume: 53 Issue: 15 Pages 7999-8008 2014
  
• Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding
  Di Palma F., Colizzi F., Bussi G.
  BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  
• Sodium-Galactose Transporter: The First Steps of the Transport Mechanism Investigated by Molecular Dynamics
  Bisha I., Rodriguez A., Sgrignani J., Magistrato A., Laio A.
  BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  
• Mechanism of Ionic Permeation in the Mimics of CNG Channels: A Structural, Functional and Computational Analysis
  Napolitano L. M. R., Bisha I., Arcangeletti M., Marchesi A., De March M., Onesti S., Laio A., Torre V.
  BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  
• Driving knots on DNA with AC/DC electric fields: topological friction and memory effects
  Di Stefano M., Tubiana L., Di Ventra M., Micheletti C.
  SOFT MATTER Volume: 10 Issue: 34 Pages 6491-6498 2014
  

2013

• BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
  Sarti E., Zamuner S., Cossio P., Laio A., Seno F., Trovato A.
  COMPUTER PHYSICS COMMUNICATIONS Volume: 184 Issue: 12 Pages 2860-2865 2013
  
• Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
  Polles G., Indelicato G., Potestio R., Cermelli P., Twarock R., Micheletti C.
  PLOS COMPUTATIONAL BIOLOGY Volume: 9 Issue: 11 2013
  
• Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
  Di Palma F., Colizzi F., Bussi G.
  RNA-A PUBLICATION OF THE RNA SOCIETY Volume: 19 Issue: 11 Pages 1517-1524 2013
  
• Sodium-Galactose Transporter: first steps of transport mechanism investigated by molecular dynamics
  Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
  EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 42 2013
  
• Development of Electrochemical Impedance Immunosensors as Point of Care Medical Diagnostic Tools
  Ianeselli L., Grenci G., Tormen M., Casalis L., Laio A.
  EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 42 2013
  
• Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations
  Franco D., Sgrignani J., Bussi G., Magistrato A.
  JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 53 Issue: 6 Pages 1371-1387 2013
  
• Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics
  Granata D., Camilloni C., Vendruscolo M., Laio A.
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 110 Issue: 17 Pages 6817-6822 2013
  
• Conformational transitions in adenine sensing riboswitch: A computational study
  Di Palma F., Colizzi F., Bussi G.
  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY Volume: 245 2013
  
• Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
  Di Stefano M., Rosa A., Belcastro V., di Bernardo D., Micheletti C.
  PLOS COMPUTATIONAL BIOLOGY Volume: 9 Issue: 3 2013
  
• The 3.5 angstrom X-ray structure of the human connexin26 gap junction channel is unlikely that of a fully open channel
  Zonta F., Polles G., Sanasi M. F., Bortolozzi M., Mammano F.
  CELL COMMUNICATION AND SIGNALING Volume: 11 2013
  
• A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations
  Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 9 Issue: 2 Pages 1240-1246 2013
  
• Thermodynamics of an Intrinsically Disordered Protein by Atomistic Simulations
  Granata D., Baghal F. B., Camilloni C., Vendruscolo M., Laio A.
  BIOPHYSICAL JOURNAL Volume: 104 Issue: 2 2013
  

2012

• Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
  Baftizadeh, Fahimeh; Biarnes, Xevi; Pietrucci, Fabio; Affinito, Fabio; Laio, Alessandro
  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 134 Issue: 8 Pages: 3886-3894 2012
  
• Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment
  Bosco, Alessandro; Bano, Fouzia; Parisse, Pietro; Casalis, Loredana; DeSimone, Antonio; Micheletti, Cristian
  NANOSCALE Volume: 4 Issue: 5 Pages: 1734-1741 2012
  
• The role of stochasticity in a model of retinal angiogenesis
  Capasso, Vincenzo; Morale, Daniela; Facchetti, Giuseppe
  IMA JOURNAL OF APPLIED MATHEMATICS Volume: 77 Issue: 6 Pages: 729-747 2012
  
• A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation
  Chiriano, Gianpaolo; De Simone, Angela; Mancini, Francesca; Perez, Daniel I.; Cavalli, Andrea; Bolognesi, Maria Laura; Legname, Giuseppe; Martinez, Ana; Andrisano, Vincenza; Carloni, Paolo; Roberti, Marinella
  EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY Volume: 48 Issue: -- Pages: 206-213 2012
  
• A simple and efficient statistical potential for scoring ensembles of protein structures
  Cossio, Pilar; Granata, Daniele; Laio, Alessandro; Seno, Flavio; Trovato, Antonio
  SCIENTIFIC REPORTS Volume: 2 Issue: -- Pages: --- 2012
  
• Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA
  Do, Trang N.; Ippoliti, Emiliano; Carloni, Paolo; Varani, Gabriele; Parrinello, Michele
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 2 Pages: 688-694 2012
  
• Exploring the low-energy landscape of large-scale signed social networks
  Facchetti, G.; Iacono, G.; Altafini, C.
  PHYSICAL REVIEW E Volume: 86 Issue: 3 Pages: --- 2012
  
• Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
  Facchetti, G.; Zampieri, M; Altafini, C.
  BMC Systems Biology Volume: 6 Issue: 1 Pages: 115 2012
  
• A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
  Ghaemi, Zhaleh; Minozzi, Manuela; Carloni, Paolo; Laio, Alessandro
  JOURNAL OF PHYSICAL CHEMISTRY B Volume: 116 Issue: 29 Pages: 8714-8721 2012
  
• Interactions of iron-sulfur clusters with small peptides: insights into early evolution
  Hong Enriquez, Rolando P; Do, Trang N
  Computational biology and chemistry Volume: 41 Issue: -- Pages: 58-61 2012
  

2011

• Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
  Cossio, P.; Laio, A.; Pietrucci, F.
  PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 13 Issue: 48 Pages: 21648-21649 2011
  
• Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations
  Rossetti, G.; Cossio, P.; Laio, A.; Carloni, P.
  FEBS LETTERS Volume: 19 Pages: 3086-3089 2011
  
• Probing the Entanglement and Locating Knots in Ring Polymers: A Comparative Study of Different Arc Closure Schemes
  Tubiana, L.; Orlandini, E.; Micheletti, C.
  PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT Issue: 91 2011
  
• Multiscale Entanglement in Ring Polymers under Spherical Confinement
  Tubiana, L.; Orlandini, E.; Micheletti, C.
  PHYSICAL REVIEW LETTERS Volume: 107 Issue: 18 Page: 188302 2011
  
• Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology
  Rosa, A.; Orlandini, E.; Tubiana, L.; Micheletti, C.
  MACROMOLECULES Volume: 44 Issue: 21 Pages: 8668-8680 2011
  
• Theoretical Studies of Homogeneous Catalysts Mimicking Nitrogenase
  Sgrignani, J.; Franco, D.; Magistrato, A.
  MOLECULES Volume: 16 Issue: 1 Pages: 442-465 2011
  
• Computing global structural balance in large-scale signed social networks
  Facchetti, Giuseppe; Iacono, Giovanni; Altafini, Claudio
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 108 Issue: 52 Pages: 20953-20958 2011
  
• Synthesis of Monomeric Derivatives To Probe Memoquin's Bivalent Interactions
  Bolognesi, M.; Chiriano, G.; Bartolini, M.; Mancini, F.; Bottegoni, G Maestri, V.; Czvitkovich, S.; Windisch, M.; Cavalli, A.; Minarini, A.; Rosini, M.; Tumiatti, V.; Andrisano, V.; Melchiorre, C.
  JOURNAL OF MEDICINAL CHEMISTRY Volume: 54 Issue: 24 Pages: 8299-8304 2011
  
• Shaping substrates at the nanoscale for single cell characterization
  Corvaglia, S.; Ianeselli, L.; Cesselli, D.; Beltrami, A.; Scoles, G.; Scaini, D.; Casalis, L.
  EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 40 Page: 226 2011
  
• Selective bio-functionalization of electrodes inside micro and nano fluidic channels
  Ianeselli, L.; Casalis, L.; Silvestrini, M.; Grenci, G.; Tormen, M.; Scoles, G.
  EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 40 Page: 228 2011
  
• Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts
  Bongarzone, S.; Tran, H.N.A.; Cavalli, A.; Roberti, M.; Rosini, M.; Carloni, P.; Legname, G.; Bolognesi, M.L.
  CHEMMEDCHEM Volume: 6 Issue: 4 Page: 601-605 2011
  
• Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE-1 Inhibitors
  Chiriano, G.; Sartini, A.; Mancini, F.; Andrisano, V.; Bolognesi, M.L.; Roberti, M.; Recanatini, M.; Carloni, P.; Cavalli, A.
  CHEMICAL BIOLOGY & DRUG DESIGN Volume: 77 Issue: 4 Pages: 268-271 2011
  
• The concept of privileged structures in rational drug design: focus on acridine and quinoline scaffolds in neurodegenerative and protozoan diseases
  Bongarzone, Salvatore; Bolognesi, Maria Laura
  EXPERT OPINION ON DRUG DISCOVERY Volume: 6 Issue: 3 Pages: 251-268 2011