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1

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

Giorgetti, Luca, Galupa, Rafael, Nora, Elphège P., Piolot, Tristan, Lam, France, Dekker, Job, Tiana, Guido, Heard, Edith

Journal:

Year:

2014

Language:

english

File:

PDF, 2.91 MB

english, 2014

2

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

Tiana, Guido, Amitai, Assaf, Pollex, Tim, Piolot, Tristan, Holcman, David, Heard, Edith, Giorgetti, Luca

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 1.85 MB

english, 2016

3

Effect of disorder on the contact probability of elongated conformations of biopolymers

Journal:

Physical Review E

Year:

2015

Language:

english

File:

PDF, 259 KB

english, 2015

4

Properties of low-dimensional collective variables in the molecular dynamics of biopolymers

Meloni, Roberto, Camilloni, Carlo, Tiana, Guido

Journal:

Physical Review E

Year:

2016

Language:

english

File:

PDF, 2.11 MB

english, 2016

5

Epigenetics and Systems Biology || From Chromosome Conformation Capture to Polymer Physics and Back

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

6

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations

Fabio Simona, Guido Tiana, Ricardo A. Broglia, Giorgio Colombo

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 528 KB

english, 2004

7

Similar folds with different stabilization mechanisms: the cases of prion and doppel proteins

Stefano Colacino, Guido Tiana, Giorgio Colombo

Journal:

BMC Structural Biology

Year:

2006

Language:

english

File:

PDF, 4.56 MB

english, 2006

8

Design and folding of dimeric proteins

Guido Tiana, Ricardo A. Broglia

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 300 KB

english, 2002

9

β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations

Isabella Daidone, Fabio Simona, Danilo Roccatano, Ricardo A. Broglia, Guido Tiana, Giorgio Colombo, Alfredo Di Nola

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 576 KB

english, 2004

10

The determinants of stability in the human prion protein: Insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions

Stefano Colacino, Guido Tiana, Ricardo A. Broglia, Giorgio Colombo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 425 KB

english, 2006

11

Exploring the protein G helix free-energy surface by solute tempering metadynamics

Carlo Camilloni, Davide Provasi, Guido Tiana, Ricardo A. Broglia

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 573 KB

english, 2008

12

Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools

Martina Caldarini, Ludovico Sutto, Carlo Camilloni, Francesca Vasile, Ricardo A. Broglia, Guido Tiana

Journal:

European Biophysics Journal

Year:

2010

Language:

english

File:

PDF, 784 KB

english, 2010

13

Understanding the determinants of stability and folding of small globular proteins from their energetics

Guido Tiana, Fabio Simona, Giacomo M.S. De Mori, Ricardo A. Broglia, Giorgio Colombo

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 188 KB

english, 2004

14

Early events in protein folding: Is there something more than hydrophobic burst?

Carlo Camilloni, Ludovico Sutto, Davide Provasi, Guido Tiana, Ricardo A. Broglia

Journal:

Protein Science

Year:

2008

Language:

english

File:

PDF, 522 KB

english, 2008

15

Design of HIV-1-PR inhibitors that do not create resistance: Blocking the folding of single monomers

Ricardo A. Broglia, Guido Tiana, Ludovico Sutto, Davide Provasi, Fabio Simona

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 621 KB

english, 2005

16

Sequence of events in folding mechanism: Beyond the Gō model

Ludovico Sutto, Guido Tiana, Ricardo A. Broglia

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 800 KB

english, 2006

17

A Highly Compliant Protein Native State with a Spontaneous-like Mechanical Unfolding Pathway

Heidarsson, Pétur O., Valpapuram, Immanuel, Camilloni, Carlo, Imparato, Alberto, Tiana, Guido, Poulsen, Flemming M., Kragelund, Birthe B., Cecconi, Ciro

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

18

Kinetics of Different Processes in Human Insulin Amyloid Formation

Mauro Manno, Emanuela Fabiola Craparo, Alessandro Podestà, Donatella Bulone, Rita Carrotta, Vincenzo Martorana, Guido Tiana, Pier Luigi San Biagio

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 2.09 MB

english, 2007

19

Corrigendum to “Kinetics of Different Processes in Human Insulin Amyloid Formation” [J. Mol. Biol. 366/1 (2007) 258-274]

Mauro Manno, Emanuela Fabiola Craparo, Alessandro Podestà, Donatella Bulone, Rita Carrotta, Vincenzo Martorana, Guido Tiana, Pier Luigi San Biagio

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

20

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

Luca Giorgetti, Trevor Siggers, Guido Tiana, Greta Caprara, Samuele Notarbartolo, Teresa Corona, Manolis Pasparakis, Paolo Milani, Martha L. Bulyk, Gioacchino Natoli

Journal:

Year:

2010

Language:

english

File:

PDF, 807 KB

english, 2010

21

Non-Cooperative Interactions Between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses To Environmental Inputs

Giorgetti, Luca, Siggers, Trevor, Tiana, Guido, Caprara, Greta, Notarbartolo, Samuele, Corona, Teresa, Pasparakis, Manolis, Milani, Paolo, Bulyk, Martha L., Natoli, Gioacchino

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 34 KB

english, 2010

22

Early Events in Insulin Fibrillization Studied by Time-Lapse Atomic Force Microscopy

Podestà, Alessandro, Tiana, Guido, Milani, Paolo, Manno, Mauro

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 475 KB

english, 2006

23

Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide

Bonomi, Massimiliano, Gervasio, Francesco L., Tiana, Guido, Provasi, Davide, Broglia, Ricardo A., Parrinello, Michele

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 934 KB

english, 2007

24

Atomistic Simulations of the HIV-1 Protease Folding Inhibition

Verkhivker, Gennady, Tiana, Guido, Camilloni, Carlo, Provasi, Davide, Broglia, Ricardo A.

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 1.11 MB

english, 2008

25

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations

Camilloni, Carlo, Broglia, Ricardo A., Tiana, Guido

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

26

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

Kimura, Sachie, Caldarini, Martina, Broglia, Ricardo A., Dokholyan, Nikolay V., Tiana, Guido

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 548 KB

english, 2014

27

A Graded Response of a Transcription Factor to Increasing Doses of External Stimuli: A Thermodynamic Framework Describing the Behavior of NF-kB

Giorgetti, Luca, Siggers, Trevor, Yaeger, Savina, Tiana, Guido, Caprara, Greta, Milani, Paolo, Bulyk, Martha L., Natoli, Gioacchino

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 50 KB

english, 2009

28

Hydrogen Bonds in Polymer Folding

Borg, Jesper, Jensen, Mogens H., Sneppen, Kim, Tiana, Guido

Journal:

Physical Review Letters

Year:

2001

Language:

english

File:

PDF, 89 KB

english, 2001

29

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers

Meloni, Roberto, Camilloni, Carlo, Tiana, Guido

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

30

Optical Absorption of a Green Fluorescent Protein Variant: Environment Effects in a Density Functional Study

Camilloni, Carlo, Provasi, Davide, Tiana, Guido, Broglia, Ricardo A.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 166 KB

english, 2007

31

Statistical analysis of native contact formation in the folding of designed model proteins

Tiana, Guido, Broglia, Ricardo A.

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 585 KB

english, 2001

32

The evolution dynamics of model proteins

Tiana, Guido, Dokholyan, Nikolay V., Broglia, Ricardo A., Shakhnovich, Eugene I.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 621 KB

english, 2004

33

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding

Tiana, Guido, Camilloni, Carlo

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.81 MB

english, 2012

34

The network of stabilizing contacts in proteins studied by coevolutionary data

Lui, Sara, Tiana, Guido

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 2.16 MB

english, 2013

35

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale

Capelli, Riccardo, Paissoni, Cristina, Sormanni, Pietro, Tiana, Guido

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1.62 MB

english, 2014

36

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations

Capelli, Riccardo, Villemot, Francois, Moroni, Elisabetta, Tiana, Guido, van der Vaart, Arjan, Colombo, Giorgio

Journal:

The Journal of Physical Chemistry Letters

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

37

Tools for the rational design of bivalent microtubule-targeting drugs

Marangon, Jacopo, Christodoulou, Michael S., Casagrande, Fancesca V.M., Tiana, Guido, Dalla Via, Lisa, Aliverti, Alessandro, Passarella, Daniele, Cappelletti, Graziella, Ricagno, Stefano

Journal:

Biochemical and Biophysical Research Communications

Year:

2016

Language:

english

File:

PDF, 2.06 MB

english, 2016

38

SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold

Capelli, Riccardo, Marchetti, Filippo, Tiana, Guido, Colombo, Giorgio

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 613 KB

english, 2017

39

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

Zhan, Yinxiu, Mariani, Luca, Barozzi, Iros, Schulz, Edda G., Blüthgen, Nils, Stadler, Michael, Tiana, Guido, Giorgetti, Luca

Journal:

Genome Research

Year:

2017

Language:

english

File:

PDF, 1.45 MB

english, 2017

40

Cold Denaturation of the HIV-1 Protease Monomer

Rösner, Heike I., Caldarini, Martina, Prestel, Andreas, Vanoni, Maria A., Broglia, Ricardo A., Aliverti, Alessandro, Tiana, Guido, Kragelund, Birthe B.

Journal:

Year:

2017

Language:

english

File:

PDF, 851 KB

english, 2017

41

How likely are oscillations in a genetic feedback loop with delay?

Cola, Filippo, Marchetti, Filippo, Tiana, Guido

Journal:

The European Physical Journal E

Year:

2017

Language:

english

File:

PDF, 881 KB

english, 2017

42

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

Capelli, Riccardo, Tiana, Guido, Camilloni, Carlo

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 3.21 MB

english, 2018

43

A method for partitioning the information contained in a protein sequence between its structure and function

Possenti, Andrea, Vendruscolo, Michele, Camilloni, Carlo, Tiana, Guido

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

44

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells

Vasile, Francesca, Panigada, Maddalena, Siccardi, Antonio, Potenza, Donatella, Tiana, Guido

Journal:

International Journal of Molecular Sciences

Year:

2018

Language:

english

File:

PDF, 1.50 MB

english, 2018

45

Spontaneous domain formation in disordered copolymers as a mechanism for chromosome structuring

Negri, Matteo, Gherardi, Marco, Tiana, Guido, Cosentino Lagomarsino, Marco

Journal:

Year:

2018

Language:

english

File:

PDF, 3.33 MB

english, 2018

46

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, Josef, Zhan, Yinxiu, Valdes-Quezada, Christian, Kryzhanovska, Mariya, Guerreiro, Isabel, Iesmantavicius, Vytautas, Pollex, Tim, Grand, Ralph S., Mulugeta, Eskeatnaf, Kind, Jop, Tiana, Guido,

Journal:

Nature Structural and Molecular Biology

Year:

2019

Language:

english

File:

PDF, 6.98 MB

english, 2019

47

Determination of Structural Ensembles of Flexible Molecules in Solution from NMR data Undergoing Spin Diffusion

Vasile, Francesca, Tiana, Guido

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 1.25 MB

english, 2019

48

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, Josef, Zhan, Yinxiu, Valdes-Quezada, Christian, Kryzhanovska, Mariya, Guerreiro, Isabel, Iesmantavicius, Vytautas, Pollex, Tim, Grand, Ralph S., Mulugeta, Eskeatnaf, Kind, Jop, Tiana, Guido,

Journal:

Nature Structural and Molecular Biology

Year:

2019

File:

PDF, 6.98 MB

2019

49

Assessing the accuracy of direct-coupling analysis for RNA contact prediction

Cuturello, Francesca, Tiana, Guido, Bussi, Giovanni

Journal:

Year:

2020

Language:

english

File:

PDF, 4.93 MB

english, 2020

50

Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential

Terzoli, Sara, Tiana, Guido

Journal:

Journal of Physical Chemistry B

Year:

2020

File:

PDF, 3.93 MB

2020