Curriculum Vitae : Flavio Seno
Personal data
Born in Feltre (Belluno), 30 July 1962
Italian citenzenship
Married, three children
Degrees
Degree in Physics, Padua University, 10 July 1987 with the mark “110/110 cum laude”
Ph. D, in Physics (Padua University) with the highest distinction (final exam in Rome 23
September 1992).
National Scientific Habilitation to Full Professor in Theoretical Physics (02/A2), Theoretical
Condensed Matter (02/B2) and Applied Physics (02/B3) obtained in 2012.
Positions
December 1987 – July 1988: visiting student at the Katholieke Universiteit di Leuven, following
the Ph.D. courses.
November 1988 – October 1991: Ph.D. student at Padua University
4 September 1991 – 19 December 2002: Researcher (Ricercatore Universitario) at the Science
Faculty of Padua University). The position was confirmed on 5th September 1994.
20 December 2002 - : Associate Professor at the Faculty of Science of Padua University.
(Certification was obtained at SISSA-Trieste in January 2001).
1
March 1992 - February 1994: post-doctoral position (on sabbatical leave) at the Department of
Theoretical Physics of Oxford University.
July 1988 - July 1989: Military service
Fellowships
A “Fondazione A. Gini” fellowship, used for three months at the Leuven Katholieke Universiteit,
in the period 1987-1988;
A “Fondazione A. Dalla Riccia”, fellowship used for 5 months at the Leuven
Universiteit in the period 1987-1988;
Katholieke
A European Fellowship of the “Science Program” (EU SCIENCE fellowship) used for 24 months
at the Department of Theoretical Physics of Oxford University in the period 1992-1994.
Teaching
I have taught several courses in several Faculties and at the Ph.D. level in Physics.
The students have always rated the quality of my teaching as excellent. For example, in recent
years, for the compulsory course of Modern Physics (Introduction to Special Relativity and
Quantum Mechanics for second year students (around 100 students) in Physics I obtained the
following marks (official data of Padua University):
Global Satisfaction
Clarity in teaching
Ability to stimulate interest in the subject
8.5/10
8.8/10
9.1/10
During my teaching activity I have always tried to promote interdisciplinary courses with particular
attention to the applications of physics to biology and medicine. Following my proposal, the
Degree course in Molecular Biology at Padua introduced a second course in Physics in addition to
the basic level one. This is the only such case in Italy. I taught this course (Complements of physics
and Mathematics) for 5 years.
In 2003 I was able to promote a programme in Biophysics within the second level degree in
Physics. Since 2010 I have taught “Biological Physics” within this programme. Last year the
number of students attending the course was 25, making it the most popular among the noncompulsory courses of the Physics degree.
2
Over the years I have supervised 40 thesis (vecchio ordinamento, laurea triennale and magistrale
and dottorato). Among my student I mention Cristian Micheletti who is now Full Professor in
SISSA and Antonio Trovato who is now Associate Professor in Padova.
Below is a detailed list of my teaching, year by year:
Exercises:
A.A. 1991/92: “Struttura della Materia”.Degree in Astronomy;
A.A. 1993/94, A.A. 1994/95, A.A. 1995/96, A.A. 1996/97: “Fisica Generale I” - Degree in
Electronic Engineering.
A.A.1991/92, A.A. 1993/94:“Laboratorio di Fisica II”. Degree in Mechanical and Civil
Engineering.
A.A. 1997/1998, A.A. 1998/1999, A.A. 1999/2000, A.A. 2000/2001: “Struttura della Materia”.
Degree in Physics .
Full courses:
A.A. 1994/95: “Meccanica Statistica”. Ph. D. in Physics.
A.A. 1997/1998: “Fisica dello Stato Solido” Diploma in Chemical Engineering.
.A.A. 1998/1999, A.A. 1999/2000, A.A. 2000/2001, A.A. 2001/2002, A.A.2002/2003 “Struttura
della Materia”. Degree in Materials Science.
A.A. 2001/2002: “Metodi Matematici della Fisica”. Degree in Materials Science.
A.A. 2002/2003, A.A. 2003/2004, A.A. 2004/2005, A.A. 2005/2006, A.A. 2006/2007: “Fisica
Quantistica della Materia (mod. A e mod. B)”.Degree in Materials Science.
A.A. 2003/2004, A.A. 2004/2005, A.A. 2005/2006, A.A. 2006/2007,A.A. 2007/2008, A.A.
2008/2009: “Complementi di Matematica e Fisica Biologica”. Degree in Molecular Biology.
A.A. 2006/2007, A.A 2007/2008, A.A. 2008/2009: “ Fisica 5 “(Introduction to Quantum
Mechanics”), Degree in Physics.
A.A. 2009/2010,A.A. 2010/2011, A.A. 2011//2012, A.A 2012/2013, A.A. 2013/2014: “Fisica
Moderna”. Degree in Physics.
A.A. 2009/2010,A.A. 2010/2011, A.A. 2011//2012,A.A 2012/2013, A.A. 2013/2014, A.A.
2014/2015: “Fisica Biologica”. Degree in Physics (II level)
A.A. 2014/2015: ‘Fisica Moderna”. Degree in Mathematics (II level)
3
Invited Talks
I have given seminars at several Italian and foreign Universities and Scientific Institutions.
On invitation I gave (or I am going to give) the following talks at International Conferences (last
10 years):
At the Workshop “Convegno di Meccanica Statistica e Teoria dei Campi non Perturbativa”. Bari
(Italy), April 1990;
At the conference “Statistical Mechanics of Soft Condensed Matter”. Firenze (Italy), May 1992;
At the Meeting “LaMBE users meeting”. Oxford (UK ), July 1993;
At the School “Recent Advances in Statistical Physics”. Istanbul (Turkey), August 1993;
At the Meeting “Convegno di Fisica Teorica e Struttura della Materia”. Fai della Paganella
(Italy), April1994;
At the meeting “Problemi attuali di Fisica Teorica”. Vietri sul Mare (Italy), April 1996;
At the National Meeting of the Italian Condensed Matter Society “Congresso Nazionale dell'
Istituto Nazionale di Fisica della Materia”. Chia Laguna (Italy), May 1997;
At the School “Scuola Nazionale di Biofisica Pura ed Applicata”. Venezia (Italy), October 1997;
At the School “Scuola Nazionale di Fisica della Materia”. Torino (Italy), September 1997;
At the meeting “Simposio sul Protein Folding”. S. Michele al Cimino (Italy), October 1997;
At the “Workshop in Protein Folding”. ISI-Villa Gualino Torino (Italy), February 1998;
At the Convegno “ Problemi attuali di Fisica Teorica”. Vietri sul Mare (Italy), April 1998;
At the “Meco 23 (Middle European Cooperation in Statistical Physics)”. ICTP - Trieste, (Italy)
April 1998;
At the National meeting of Italian Physical Society “LXXXIV Congresso Nazionale della SIF”.
Salerno (Italy), September 1998;
at “Gran Sasso Workshop 99: Summer Institute on Numerical Simulations of Field Theories”.
INFN National Laboratories , Gran Sasso ( Italy) , July 1999;
at the “IX Workshop on Computational Material Science (CMS99)”. Villasimius (Italy), September
1999;
4
at the “Workshop on Protein Structure”, during the meeting “Mathematical Methods for Protein
Structure Analysis and Design”, Martina Franca (Italy), July 2000;
at the meeting “Convegno della Società Italiana di Biofisica Pura e Applicata”. Parma (Italy),
October 2000;
at the Conference “Protein Folding and Design I”. Trieste (Italy), May 2001;
at the Conference “Biophysics of Membranes”. Trieste (Italy), September 2001;
at the Workshop “Bioinformatics and Statistical Physics”. Saarbrucken (Germany), October 2002;
at the Conference “Protein Folding and Design II”. Trieste (Italy), May 2003;
at the CECAM
September 2003;
Workshop “Statistical mechanics of random copolymers”. Lyon (France),
at “4th International Workshop on Structural Characterisation of Proteins by NMR, X-ray
Diffraction and Computational Methods”. San Vito di Cadore (Italy) , May 2004;
at the International Conference “From Solid State to Biophysics II: Role of Inhomogeneities in
Solid, Soft and Bio-Matter”. Dubrovnik (Croatia), June 2004;
at the Workshop “Bioinformatics and Statistical Physics”. Glasgow (UK), July 2004;
at the “XIV Workshop on Computational Material Science ”. Geremeas (Italy) , September 2004;
at the
“International Workshop on Statistical Mechanics and Combinatorics: Counting
Complexity”. Dunk Island (Australia), July 2005;
at the Meeting “Selected Topics in Nuclear and Atomic Physics”. Fiera di Primiero (Italy),
October 2005;
At the “Workshop on the Structure and Function of Biomolecules II”. Bedlewo (Poland), May
2006;
At the conference “Modelling elastic manifolds, from soft condensed matter to biomolecules".
Trieste (Italy), July 2006;
At the “5th International Workshop on Structural Characterisation of Proteins by NMR, X-ray
Diffraction and Computational Methods”. San Vito di Cadore (Italy ), July 2006;
At the CECAM Workshop “Protein folding and misfolding: Bringing theory close to experiment
and vice versa”. -Lione (France ) September 2006;
At the Congress “STATPHYS-KOLKATA VI” . Kolkata (India), January 2007;
At the Workshop “Physics and Biology: a sinergy”. Hyderbad (India), December 2007;
5
At the Conference “Knots and Macromolecules II”. Venice (Italy), March 2008;
At the Conference “From Solid State to Biophysics IV”. Dubrovnik (Croatia), June 2008;
At the Conference “BIT Life Sciences' 2nd Annual Protein and Peptide Conference”. Seoul (South
Korea) , March 2009 ;
At the Conference "Statistical Physics of Lattice Polymers". Melbourne (Australia), July 2009;
At the Conference “Pepcon-2011: New Leaders in Protein and Peptide Science”, Beijing (China),
March 2011;
At the Workshop
October (2001);
“NANOTECHNOLOGY MEETS CLINICAL MEDICINE”, Aviano (Italy)
At the Workshop “Means, Methods and Results in the Statistical Mechanics of Polymeric
Systems”, Toronto (Canada), June 2012;
At the “International Summer School on Fundamental Problems in Statistical Physics XII” Leuven
(Belgium). 16-29 June 2013;
At the “1st International Workshop on Theoretical and Computational Physics”: Da Nang
(Vietnam) 30 July-2 August 2013;
At the Workshop “Living systems: from interactions patterns to critical behaviour”: Venice 16-19
September 2015.
At the Workshop “Computational approaches in QFT, Statistical Mechanics and Complex
System”, Bari 9-11 December 2015
Organization of Conferences
I organized with Anne Chaka (NIST , Washington) the Euresco Conference:
“Biophysics from First Principles: From the Electronic to the Mesoscale”
San Feliu de Guixols (Spain), 7-12 September 2002.
I was named chairman of the Biophysics Section of the:
“Psi-K Conference” Schwabisch Gmund (Germany) 22 -26 August 2000.
I organized the workshop
“Fisica Statistica di Bioplomieri“ during the National Meeting of the Italian Condensed Matter
Society (INFMeeting) , June 2002.
I organized (with Silvio Tosatto, Padova)the Workshop:
“Predicting the Structure and Function of Proteins“, Padova (Italy) 10 -11 December 2004.
6
I organized (with Enzo Orlandini (Padova), Enrico Carlon (Leuven), Jospeh Indekeu (Leuven) the
Workshop
“Interdisciplinary Topics in Statistical Physics”, Venice (Italy) 16-18 April 2009.
I organized (with Guido Tiana, Milano) the Workshop
“Physics of Protein Folding and Aggregation” Brixen (Italy) 11-12 February 2010.
I organized the Workshop: “Biophysics” Larnaka (Cipro), 11-15 July 2011, within the Sigma-Phi
2011 Conference.
I organized (with Guido Tiana, Milano) the Workshop:
“Physics of Protein Folding and Aggregation II” Brixen (Italy), 16-18 February 2012.
I organized (with R.Metzler, Postdam) the Conference:
“Fluctuation on small complex systems” Venezia (Italy) , 21-24 October 2012.
I organized (with R.Metzler, Postdam) the Conference:
“Fluctuation on small complex systems II” Venezia (Italy) , 10-13 October 2014.
I am organizing (President of the Steering Committee) the FisMat2015, the Italian National
Conference on Condensed Matter Physics which will take place in Palermo (Sicily) from
September 28th to October 2nd , 2015.
In 2004 (with Silvio Tosatto, Padova) I started the organization of interdisciplinary monthly
meetings (P2P seminars) with the official support of Departments of Physics, Biology, Chemistry
(Faculty of Science), Chemical Biology (Faculty of Medicine) and of the Faculty of Engineering.
The meetings (a full afternoon) continued for 5 years, with an average participation of 100 persons
from the different Departments.
Managment of scientific and educational activities
1994 - 2001: Member of the Scientific Commission (Area 02 Physical Sciences) of the Padua
University.
1994 - 2004 : Member of the Commission For the planning of Laurea thesis activity of the Physics
Department of Padua
1994 - 1997 : Representative of Padua Group in the Board (Sezione Ristretta)
of the G-Section (Theory) of the National Institute for Matter Physics (INFM)
In 1997 I opened the Biophysics Group of INFM at Padua University and from then, till the
closure of INFM, I was the representative of the group in the National Board (Sezione Ristretta)
of the Biophysics Section
1998 - 2001: Member of the Local Board (Consiglio di Unitá) of the INFM in Padua.
7
1999 - 2003: Person in charge of the ERASMUS/SOCRATES exchanges between Padua and
Oxford Universities
1999 – 2004: Member of the “Didactical Commission” of the Laurea degree in Material Sciences.
1999 - 2003: Member of the “Special Commission”(6 persons) in charge of redefining the degree
programme in Material Science according the new scheme (3+2).
2004 - 2006
: Chairman of the “Comitato Ordinatore del Corso di Laurea in Ottica ed
Optometria” of the University of Padua (Committee in charge of creating the new degree course)
2004-2006 : Member of the Board (Consiglio di Presidenza) of the Faculty of Science of Padova
University
2006- 2009 : Member of the Council (Giunta) of the Physics Department of Padua University;
2008 - 2011 : Representative of the Rector of Padua University in the National Assembly of
CNISM (Consorzio Nazionale Interuniversitario per le Scienza Fisiche della Materia).
2008- 2011 : Director of the Padova Unity of CNISM.
2011 CNISM
: Member (by election) of the Governing Body (Consiglio di Amministrazione) of
2013 University.
: Chairman of the Scientific Commission (Area 02 Physical Sciences) of the Padua
2013 University
: Member of the Scientific Panel (Commissione Scientifica di Ateneo) of the Padua
2015 : Member of the Governing Body of Collegio D.N. Mazza, one of the 14 Collegi
Universitari di Merito (such as Ghisleri and Borromeo in Pavia) officially recognized and
supported by the Italian Ministry for Education.
I have been member of a National Commission to assign a permanent research position in
Florence (2001)
I have been member of a CNISM National Commission to assign temporary research positions in
2010.
I have been member of a National Commission to assign a temporary research position (RTDa) in
Genova (2012)
N.B.: Of all my management activities, the most difficult and time-consuming was the one
regarding the opening of the new Corso di Laurea in Ottica ed Optometria. This degree was the
second to start in Italy. I had to tackle several problems from the beginning, contending with the
initial opposition of the Faculty of Medicine and the lobby of Ophthalmologists. I had to find
8
grants (and I was able to get the support of Camera di Commercio di Padova, Ascom di Padova,
Federottica), to create a completely new syllabus with new kind of student laboratories (optometry,
contact lens) and advertise to inform students all over the country of this new academic possibility.
The programme degree started in 2004/2005 and when I left the job everything was settled very
well: we had 70 applicants for 40 places on the course.
Nowadays in Italy there are 6 Corsi di Laurea in Ottica ed Optometria.
Since I am chairman of the Scientific Commission of Physical Science, the amount pro capite
obtained by our Department from a constant University budget increased from 6239 Euro (2012)
to 7750 Euro (+25%).
Grants
I won European Fellowship of the “Science Program” (EU SCIENCE fellowship) to be used in
Oxford with a supporting grant of 30000 British Pounds .
I have been local coordinator of a grant (ex 40%) (principal investigator: Prof. M. Ferrario Modena) funded in 1996.
I have been local coordinator of a PAIS Grant - Progetto Avanzato di Interesse Specifico dell'
INFM (principal investigator Prof. A. Maritan- SISSA Trieste) funded in 1997.
I have been local coordinator of a PRIN project (principal investigatort Prof. A. Maritan – SISSA
Trieste) funded in 2003.
I have been coordinator of a Padova University Grant for Fellowship (Progetto di Ateneo per
assegni di ricerca) funded in 2003.
I have been coordinator of a Padova University Grant (Progetto di Ateneo) funded in 2008.
I was participant in PRIN projects granted in 1999, 2001, 2005, 2007, 2009 and 2012.
Other activities
I am referee of the following journals: Physical Review B, Physical Review E, Physica, Physical
Review Letters, Journal of Chemical Physics, Journal of Physics, Biophysical Journal, Proteins,
FEBS Letters, Journal of Theoretical Biology.
I was Guest Editor of the special issue "New trends in modern statistical physics" of Centr. Eur. J.
Phys 10 (June 2012)
I have been an external examiner for several Ph.D. students in Italy. Abroad, I have been on
doctoral examining committees at the University of Oxford (July 1996) , University of Toronto
(June 2008), University of Lausanne (December 2011) , University of Varanasi (July 2012) and
University of Lund (February 2014)
9
I was invited as visiting Professor (Maitre de Conferences Invitè) to the Universite Henry Poincaré
(Laboratoire de Physique du Solide), Nancy (July 1997) where I gave the course “An introduction
to the statistical properties of polymers and proteins”.
I was invited as visiting Professor (Maitre de Conferences Invite) to the University of CergyPointoise, Paris (July 2003).
I am co-author of a paper: “An optimal protein design procedure”, F. Seno, M. Vendruscolo, A.
Maritan e J.R.Banavar, Phys. Rev. Lett. 77, 1901-1904 (1996) that was selected as INFM
“highlight for the period 1996-1997.
I am co-author of a paper “Design of proteins with hydrophobic and polar amino-acids.”, C.
Micheletti, F. Seno, A. Maritan e J.R.Banavar, PROTEINS: Struct. Funct. and Gen. 32, 80-87
(1998) which was selected as “Highlight of Biophysics Section of INFM ” for 1998.
I am co-author of the paper “Exploring the universe of protein folds beyond the protein data bank”.
P. Cossio, A. Trovato, F. Pietrucci, A. Maritan, F. Seno and A. Laio, Plos Computational Biology
11 , e1000957 (2010), which was selected as Highlight of CNR for the period 2009-2010.
Patents and licences
I am coauthor (with Silvio Tosatto and Antonio Trovato) of the software PASTA, the licence for
which was sold, in 2012, by Padua University to the pharmaceutical society Boehringer
Ingelheim. The software aims to predict which portion of a protein sequence is more prone to form
a fibrillar aggregate. The software is based on the scientific publications:
A. Trovato, F. Chiti, A. Maritan and F. Seno, Plos Computational Biology 12, 1608-1618 (2006)
A. Trovato, F. Seno and S.C.E. Tosatto, Protein Engineering Design and Selection 20, 521-523
(2007)
Research activity
In the early years of my career, I worked on topics related to critical phenomena and phase
transitions. Starting in 1996, I oriented my research towards the application of statistical mechanics
to biological problems with particular attention to medical and pharmaceutical applications.
The main results I obtained are:
10
Solution of the theta point problem:
We were able to determine numerically the bulk[a] and surface[b,c] exponents for linear polymers
at the theta point, in 2 dimensions. These results stimulated a strong debate since they were in
contradiction with the existing theory proposed by Duplantier and Saleur [Phys. Rev. Lett. 59, 3617
(1987)]. Later, we were able to solve the problem exactly[d] by using a mapping on a percolative
problem in the presence of a boundary. These results have been completely accepted by the
scientific community as the complete solution of the theta point problem and quoted in many
reviews, e,g. K. De’Bell and T. Lookman [Surface phase transitions in polymer systems in
Reviews of Modern Physics, 65 87, (1993)], and E. Eisenrigler [Polymers near a surface:
conformation properties and relation to critical phenomena, Singapore, World Scientific, (1993)]
and in the books: C. Vanderzande [Lattice Models of Polymers, Cambridge University Press, 1998]
and M. Henkel [Conformal invariance and critical phenomena, Berlin, Springer (1999)].
[a] F. Seno, A.L. Stella, J. Physique, Vol.49, pp.739-748 (1988)
[b] F. Seno, A.L.Stella, C. Vanderzande, Phys. Rev. Lett., Vol.61, pp.1520 (1988)
[c] F. Seno, A.L. Stella Europhys. Lett., Vol. 7, pp.605-610 (1988)
[d] C.Vanderzande, A.L. Stella, F. Seno, Phys. Rev. Lett Vol. 67, pp.2757-2760 (1991),
Protein design:
We introduced[a] a general method for protein design based on an analysis in sequence space of the
Boltzmann weight for a given target structure. We introduced different approaches to implement
this method. In particular, by using a free energy expansion based on the amino acid
concentrations[b] we were able to successfully design on a cubic lattice (Harvard- San Francisco
test) 10 structures of length 48 within the hydrophobic polar (HP) classification of the amino acids.
With the same classification of the amino acids, we generalized[c] the method to design real
proteins with a success rate of 75% . These results were highlighted in the divulgation journals
“Scientific Computing World” (April 1998, p. 8) and “Le Scienze” (July 1998, p. 15).
[a] F.Seno, M. Vendruscolo, A. Maritan, J.R. Banavar, PRL 77, pp.1901-1904 (1996)
[b] C. Micheletti, F. Seno, A. Maritan and J.R. Banavar , PRL 80, pp.2237-2240 (1998)
[c] C. Micheletti, F. Seno, A. Maritan and J.R. Banavar, Proteins: Structure, Function, and
Genetics, 32, pp 80-87 (1998)
Topological properties of proteins:
In the work [a] we demonstrated the important role played by the geometrical and topological
properties of the native state in determining the folding properties of a protein. Strikingly, by
studying the conformational entropy of a backbone it was possible to identify the peptide regions
that come in contact at early stages of folding with no detailed information on the sequences that
are housed in the target fold. These results regarding the folding nucleus are fully consistent with
experimental findings. Even today, this paper is still regularly quoted in the literature (more than
110 citations).
Later on , we introduced a novel and fully automated criteria for an optimal partitioning of a
complete data bank of protein fragments . We proved that with only a few dozen of such fragments
(length 6 aminoacids), virtually any protein can be reproduced within typical experimental
uncertainties.
[a]C. Micheletti, J.R. Banavar, A. Maritan and F. Seno PRL 82, pp. 3372-3375 (1999)
[b] C. Micheletti, F. Seno, A. Maritan, Proteins 40, 662 (2000)
11
General framework to understand the structural properties of proteins:
In a set of papers[a,b,c] we proposed that native-state folds of proteins can emerge on the basis of
considerations of geometry and symmetry. We showed that the inherent anisotropy of a chain
molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and
hydrophobicity are sufficient to yield a free-energy landscape with broad minima even for a
homopolymer. These minima correspond to marginally compact structures comprising the menu of
folds that proteins choose from to house their native states. This result justifies the well-known fact
(Denton and Marshall Nature 410, 417, 2001) that the number of protein folds is limited and not
subject to evolution. The fact that possible folds can be determined only by using a homopolymer
was confirmed in a more recent paper [d]. Using a sophisticated numerical approach, we
performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide
chain described with an accurate all-atom interaction potential. We found an ensemble of almost
7000 independent structures in which it is possible to find all the folds which are known for similar
lengths. However, the ensemble of known folds forms a relatively small corner of this ensemble.
Many more proteins are possible. Our analysis suggests that existing proteins were evolutionarily
selected under the guidance of a simple principle: reducing the entanglement in the bundle formed
by the protein in its folded state. This makes bundles with shorter loops preferable. The set of
structures that we make available will potentially open a range of practical applications in
biomedical sciences.
[a] T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar and A. Maritan, PNAS USA, Vol. 101, pp.
7960-7964 (2004)
[b]J.R. Banavar, T.X. Hoang, A. Maritan, F. Seno and A. Trovato, PRE 70, art. N. 041905 (2004)
[c] T.X. Hoang, L. Marsella, A. Trovato, F. Seno, J.R. Banavar and A. Maritan, PNAS USA 103,
6883-6888 (2006)
[d] P. Cossio, A. Trovato, F. Pietrucci, A. Maritan, F. Seno and A. Laio, Plos Computational
Biology 11 , e1000957 (2010)
Interaction potentials for Protein Folding:
An essential ingredient for understanding protein folding and design is the task of deducing the
coarse-grained potentials of interaction between the amino acids. In the course of my research work
I have published several papers on this topic which were well accepted by the scientific
community[a,b,c,d]. Very recently[e, f] we proposed a novel statistical potential constructed by
Bayesian analysis measuring a few structural observables on a set of 500 experimental protein
structures. Even though employing many fewer parameters than current state-of-the-art methods,
our potential is capable of discriminating with unprecedented reliability the native state in large sets
of misfolded models of the same protein.
[a] F. Seno, A. Maritan and J.R. Banavar, Proteins: Structure, Function, and Genetics 30, pp.244248 (1998)
[b] F. Seno, C. Micheletti, A. Maritan and J.R. Banavar PRL 81, pp.2172-2175 (1998)
[c] C. Micheletti, F. Seno, A. Maritan, J.R. Banavar, Proteins 42, 422 (2001)
[d] H.T. Dobbs, E. Orlandini, R. Bonaccini , F. Seno,Proteins 49, 342 (2002)
[e] P. Cossio, D. Granata, A. Laio, F. Seno, A. Trovato Scientific Reports 2, Art. No. 351 (2012)
[f] E. Sarti, S. Zamuner, P. Cossio, A. Laio, F. Seno and A. Trovato, Comp. Phys. Comm. 184,
2860 (2013)
Amyloid fibrils:
12
An increasing number of terrible human pathologies (such as Alzheimer’s and Parkinson’s
diseases) are associated with the conversion of peptides and proteins from their soluble functional
forms into well-defined fibrillar aggregates called amyloids. In ref. [a] and [b,c] we developed an
algorithm to predict the portions of a sequence, for an initially unstructured polypeptide chain, that
stabilizes the cross-beta core of the amyloid fibrils. Our predictions are extremely accurate when
compared with experimental findings and they can be used to design mutations that could mitigate
the aggregation process and therefore used for therapeutic applications. Our method is available on
a web site (http://protein.bio.unipd.it/pasta/) (16000 download). Moreover, the related software we
produced (Palmo) was sold, in 2011, by Padua University to the pharmaceutical company
Boehringer Ingelheim.
[a] A. Trovato, F. Chiti, A. Maritan and F. Seno, Plos Computational Biology 12, 1608-1618
(2006)
[b] A. Trovato, F. Seno and S.C.E. Tosatto, Protein Engineering Design and Selection 20, 521-523
(2007)
[c] I. Walsh, F. Seno, A. trovato and S.C.E. Tosatto, Nucleic acids research 42 , W301-7 (2014)
Modelling of mechanical denaturation of DNA
The recent refinements in experimental tools employing optical tweezers, atomic force microscopes
and soft microneedles make it possible to monitor the behaviour under tension and stress of
various biopolymers, and then to elucidate the mechanism of some force driven phase transitions
occurring at the single molecule level, such as the stretching of single collapsed DNA molecules,
and the unzipping of DNA. The large quantity of experimental results was demanding for
theoretical modelling. In this field we have proposed and solved, both numerically and
analytically[a,b,c,d,e] several models giving a well-recognized contribution to the field. In
particular, we have suggested [a,b] the existence of cold denaturation of a double stranded
biopolymer (e.g. DNA) under mechanical stress. Such a transition has not yet been seen
experimentally, but the accuracy of our calculation was confirmed in an extended range of
temperatures. (C. Danilowitz, Y. Kafri, R.S. Conroy et al. [Phys. Rev. Lett. 93, art. 078101
(2004)]).
[a] E. Orlandini, S.M. Bhattacharjee, D. Marenduzzo, A. Maritan, F. Seno, JPA 34, L751 (2001)
[b] D. Marenduzzo, S.M. Bhattacharjee, A. Maritan, E. Orlandini, F. Seno PRL 88, 028102 (2002)
[c]D. Marenduzzo, A. Maritan , A. Rosa and F. Seno , PRL 90 art no -088301 (2003)
[d]A. Rosa, D. Marenduzzo, A. Maritan and F. Seno ,Phys. Rev. E, Vol. 67, art. no. 041802 (2003)
[e]Kapri, S.M. Bhattacharjee and F. Seno , PRL 93, art. no248102, (2004)
Measure for data collapse.
We proposed [a] a measure to quantify the nature of data collapse, e.g for establishing scaling and
extracting the associated exponents in problems showing self-similar or self-affine characteristics,
for example, in equilibrium or non-equilibrium phase transitions . Via a minimization of this
measure, the exponents and their error bars can be obtained. The methods works remarkably well
and it has been used in a variety of problems such as the dynamics of ecological communities and
the study of biological networks.
[a] S.M. Bhattacharjee and F. Seno , J. Phys. A, Vol. 33, pp.6375-6380 (2001)
Efimov effect for polymer physics
13
We proposed [a] and directly verified on an exactly solvable model[b] that the cold atom quantum
Efimov effect, namely the possibility of a three body bound state where none of the pairs is bound,
can be observed in thermal denaturation of three strand polymeric systems. This observation might
have important and unexpected implications in a biological context where many processes
involved three polymers (e.g. three helix DNA)
[a] J. Maji, S.M. Bhattacharjje, F. Seno and A Trovato, New Journal of Physics 12, 083057 (2010)
[b] J. Maji, S.M. Bhattacharjje, F. Seno and A Trovato, Phys. Rev. E89, 012121 (2014)
Quorum sensing
Quorum sensing can be described as the regulation of gene expression in response to changes in the
bacterial population density. In this emerging field of microbiology we have introduced specific
modeling which takes into account the presence of different boundary conditions and our
calculations motivated dedicated experiments that we performed in collaboration with
experimentalists of our university (Squartini, Brun). Our results have been quoted in the book by
Stephen Hagen “The physical basis of Bacterial Quorum Communication”that is the first
monography ever written on this subject.
[a] S. Alberghini et al FEMS Microbiology Letters 292, 149-161 (2009) USA
[b] A. Trovato et al. FEMS Microbiol. Lett. 352, 198 (2014)
Bibliometric parameters (ISI Web of Science)
Total number of papers: 94
Total number of citations: 1939 (without self-citations: 1734); Google Scholar: 2466
Number of citations per article: 20.62;
Average IF (total IF/ number of papers): 3.80
H-index: 25 Google Scholar: 27
14
ELENCO COMPLETO DELLE PUBBLICAZIONI
FLAVIO SENO
1.
F. Seno, A.L. Stella
θ point of a linear polymer in 2 dimensions: a renormalization group analysis of Monte
Carlo enumerations
J. Physique, Vol.49, pp.739-748 (1988), Francia
2.
F. Seno, A.L. Stella, C. Vanderzande
Universality Class of the d=2 θ Point of Linear Polymers
Phys. Rev. Lett., Vol.61, pp.1520 (1988), USA
3.
F. Seno, A.L. Stella
Surface Exponents for a Linear Polymer at the d=2 θ Point
Europhys. Lett., Vol. 7, pp.605-610 (1988), USA
4.
Maritan, F. Seno, A.L. Stella
Real Space Renormalization Group Approach to the Theta Point of a Linear Polymer in 2
and 3 Dimensions
Physica A, Vol. 156, pp.679-688 (1989), Olanda.
5.
F. Seno, A.L. Stella
Conduction and connection properties of self--avoiding walks with bridge
Phys. Rev. A, Vol.40, pp.4704-4708 (1989), USA
6.
R. Dekeyser, F. Igloi, F. Mallezie, F. Seno
Analysis of series with stochastic coefficients
Phys. Rev. A, Vol.42, pp.1923-1930 (1990), USA.
7.
F. Seno, A.L. Stella, C. Vanderzande
Self avoiding walks in the presence of strongly correlated, annealed vacancies
Phys. Rev. Lett., Vol.65, pp.2897-2900 (1990), USA
8.
S.L.A. de Queiroz, F. Seno, A.L. Stella
Polymers on Fractals and at the θ--Point Results of Flory Approximation
J. Physique, Vol. I1, pp.339-349 (1991), Francia
9.
A. Maritan, F. Seno, A.L. Stella
Gauge model with Ising vacancies multicritical behaviour for self--avoiding surfaces
Phys. Rev. B, Vol.44, pp. R2834-2837 (1991), USA
10.
C. Vanderzande, A.L. Stella, F. Seno
Percolation, the Special θ, and the θ – θ’ Universality Puzzle
Phys. Rev. Lett Vol. 67, pp.2757-2760 (1991), USA
11.
E. Orlandini, F. Seno, A.L. Stella, M.C. Tesi
Collapse from linear to branched polymer behaviour
Phys. Rev. Lett., Vol.68, pp 488-491 (1992), USA
15
12.
M. Di Stasio, F. Seno, A.L. Stella
Vescicles on hierarchical lattice: an exact renormalization group approach
J. Phys. Vol. A25, 3891-3900 (1992), Gran Bretagna.
13.
D.P. Foster, F. Seno
Adsorption of two-dimensional vesicles
J. Phys. A, Vol.26, pp.1299-1311 (1993), Gran Bretagna
14.
F. Seno, D.A. Rabson, J.M. Yeomans
Low-Temperature Behaviour of the 6-state clock model with competing interactions
J. Phys. A , Vol.26, pp.4887-4905 (1993), Gran Bretagna
15.
A.L. Stella, F. Seno, C. Vanderzande
Boundary critical behaviour of d=2 self avoiding walks on correlated and uncorrelated
vacancies
J. Stat. Phys., Vol.73, pp.21-46 (1993), Belgio
16.
F. Seno, J.M. Yeomans, R. Harbord and D.Y.K. Ko
Ground state of a model with competing interactions and spin anisotropy
Phys. Rev. B, Vol.49, pp.6412-6415 (1994), USA
17.
F. Seno, J.M. Yeomans, R. Harbord and D.Y.K. Ko
Crossover between the discrete and the continuous spin limits in the ground state of a model
with competing interactions and spin anisotropy
Proceedings of the School “Advanced Topics in Statistical Mechanics”, Turk. Jour. of
PhysicsVol. 18, pp.361-366 (1994), Turchia
18.
F. Seno, C. Vanderzande
Non-Universality in the Collapse of two-dimensional branched polymers
J. Phys. A, Vol.27, pp 5813-5830 (1994), Gran Bretagna
19.
D.Y.K. Ko, F. Seno
Simulations of deposition growth models in various dimensions The possible importance of
overhangs
Phys. Rev. E, Vol.50, pp.R1741-1744 (1994), USA
20.
F. Seno, J.M. Yeomans
Spin softening in models with competing interactions: a new high anisotropy expansion to
all orders
Phys. Rev. B, Vol.50, pp.10385-10388 (1994), USA
21.
D.Y.K. Ko and F. Seno
Deposition growth modes from numerical simulations
Phys. Rev. B, Vol.50, pp.17583-17586 (1994), USA
22.
C. Micheletti, F. Seno, J.M. Yeomans
Upsilon point in a spin model
16
Phys. Rev. B, Vol.52, pp. 4353-4359 (1995), USA
23.
F. Seno, J.M. Yeomans
Modulated structures stabilized by spin softening: an expansion in inverse spin anisotropy
Phys. Rev. B, Vol. 52, pp.9550-9563 (1995), USA
24.
P. De Los Rios, G. Caldarelli, A. Maritan, F. Seno
Optimal path and directed percolation
Phys. Rev. E, Vol.53, pp.R2029-2032 (1996), USA
25.
M. Henkel, F. Seno
Phase diagram of branched polymer collapse
Phys. Rev. E, Vol.53, pp. 3662-3672 (1996), USA
26.
F. Seno, M. Vendruscolo, A. Maritan, J.R. Banavar
An optimal protein design procedure
Phys. Rev. Lett., Vol. 77, pp.1901-1904 (1996), USA
27.
F. Seno, A.L. Stella, C. Vanderzande
Optimal self avoiding paths in dilute random medium
Phys. Rev. E, Vol.55, pp.3859-3864 (1997), USA
28.
A. Trovato and F. Seno
Universality for interacting oriented self--avoiding walk: a transfer matrix calculation
Phys. Rev. E, Vol.56, pp.131-143 (1997), USA
29.
P. De Los Rios, A. Maritan and F. Seno
Polymers with a bimodal distribution and directed percolation
J. Phys. A, Vol. 30, pp.L617-621 (1997), UK
30.
F. Seno, A. Maritan and J.R. Banavar
Interactions potentials for Protein Folding
Proteins: Structure, Function, and Genetics, Vol.30, pp.244-248 (1998), USA
31.
C. Micheletti, F. Seno, A. Maritan and J.R. Banavar
Protein Design in a Lattice Model of Hydrophobic and Polar Amino Acids
Phys. Rev. Lett., Vol.80, pp.2237-2240 (1998), USA
32.
J.R. Banavar, M. Cieplak, A. Maritan, G. Nadig, F. Seno and S. Vishveshwara
Structure-Based Design of Model Protein
Proteins: Structure, Function, and Genetics, Vol.31, pp.10-20 (1998), USA
33.
C. Micheletti, F. Seno, A. Maritan and J.R. Banavar
Design of proteins with hydrophobic and polar aminoacids
Proteins: Structure, Function, and Genetics, Vol.32, (1998), USA
34.
C. Micheletti, J.R. Banavar, A. Maritan and F. Seno
17
Steric constraints in model proteins
Phys. Rev. Lett.,Vol.80, pp.5683-5686 (1998), USA
35.
36.
F. Seno, C. Micheletti, A. Maritan and J.R. Banavar
Variational approach to protein design and extraction of interaction potentials
Phys. Rev. Lett., Vol.81, pp.2172-2175 (1998), USA
C. Micheletti, J.R. Banavar, A. Maritan and F. Seno
Protein structures and optimal folding from a geometrical variational principle
Phys. Rev. Lett., Vol.82, pp. 3372-3375 (1999), USA
37.
J. van Mourik, C. Clementi, A. Maritan, F. Seno, J.R. Banavar
Determination of interaction potentials of amino-acids from native protein structure. Tests
on simple lattice models
J. Chem. Phys., Vol.110, pp.10123-10133 (1999), USA
38.
C. Micheletti, F. Seno, A. Maritan and J.R. Banavar
Strategies for protein folding and design
Annals of Combinatorics, Vol.3, pp.439-458 (1999), Australia
39.
R. Bonaccini and F. Seno
A simple model to study the insertion of a protein in a membrane
Phys. Rev. E, Vol.60, pp.7290-7298 (1999), USA
40.
E. Orlandini, F. Seno and A.L. Stella
Adsorption like collapse of diblock copolymers
Phys. Rev. Lett., Vol.84, pp.294-297 (2000), USA
41.
C. Micheletti, F. Seno, A. Maritan
Recurrent oligomers in proteins - an optimal scheme reconciling accurate and coincise
backbone representations in automated folding and design studies
PROTEINS: Structure, Function, and Genetics, Vol.40, pp. 662-674 (2000), USA
42.
E. Orlandini , F. Seno, J.R. Banavar, A. Laio and A. Maritan
Deciphering the folding kinetics of transmembrane helical proteins
Proceedings of the National Academy of Science (USA),Vol.97, pp.14229-14234 (2000),
USA
43.
C. Micheletti, F. Seno, A. Maritan and J.R. Banavar
Learning effective amino acid interactions through iterative stochastic techniques
PROTEINS: Structure, Function, and Genetics, Vol.42, pp.422-431 (2001), USA
44.
C. Micheletti, F. Seno, A. Maritan and J.R. Banavar
An optimal procedure to extract interaction potentials for protein folding
Journal of Computational Materials Science, Vol. 20, pp.305-310 (2001), USA
45.
A. Rossi , C. Micheletti, F. Seno and A. Maritan
Self-consistent knowledge-based approach to protein design
Biophysical Journal, Vol.80, pp.480-490 (2001), UK
18
46.
S.M. Bhattacharjee and F. Seno
A measure of data collapse for scaling
J. Phys. A, Vol. 33, pp.6375-6380 (2001), UK
47.
D.P. Foster and F. Seno
Two dimensional self-avoiding walk with hydrogen-like bonding: Phase diagram and
critical behaviour
J. Phys. A , Vol. 34, pp.9939-9957 (2001), UK
48.
D. Marenduzzo, S.M. Bhattacharjee, A. Maritan, E. Orlandini and F. Seno
Mechanical denaturation of DNA: existence of a low temperature denaturation
J. Phys. A, Vol. 34, pp.L751-L758 (2001), UK
49.
D. Marenduzzo, S.M. Bhattacharjee, A. Maritan, E. Orlandini and F. Seno
Dynamical scaling of the DNA unzipping transition
Phys. Rev. Lett., Vol.88, pp.028102-028106 (2002), USA
50.
D. Marenduzzo, A. Maritan and F. Seno
Force-induced unfolding of a homopolymer on a fractal lattice: exact results versus meanfield predictions
J. Phys. A, Vol.35, pp.L233-L240 (2002), UK
51.
J.R. Banavar, A. Maritan and F. Seno
Anisotropic Effective Interactions in a Coarse-Grained Tube Picture of Proteins
Proteins: Structure, Function and Genetics, Vol.49, pp.246-254 (2002) , USA
52.
H.T. Dobbs, E. Orlandini, R. Bonaccini and F. Seno
Optimal Potentials for Predicting Inter-Helical Packing in Transmembrane Proteins
Proteins: Structure, Function and Genetics, Vol.49, pp.342-349 (2002), USA
53.
D. Marenduzzo, A. Maritan , A. Rosa and F. Seno
Stretching of a polymer below the theta point
Phys. Rev. Lett., Vol. 90, art no -088301 (2003), USA
54.
S.M. Bhattacharjee and F. Seno
Helicase on DNA: a phase coexistence based mechanism
J. Phys. A,Vol.36, pp. L181-L187 (2003), USA
55.
A. Rosa, D. Marenduzzo, A. Maritan and F. Seno
Mechanical unfolding of directed polymers in a poor solvent: Critical exponents
Phys. Rev. E, Vol. 67, art. no. 041802 (2003), USA
56.
T.X. Hoang, F. Seno, J.R. Banavar, M. Cieplak and A. Maritan
Assembly of protein tertiary structures from secondary structures using optimized potentials
Proteins: Structure, Function and Genetics, Vol.52, pp.155-165 (2003) , USA
57.
H.T. Dobbs, L. Peruzzo, F. Seno, R. Spiess and D.J. Prior
Unraveling the Schneeberg garnet puzzle: a numerical model of multiple nucleation and
coalescence
19
Contributions to Mineralogy and Petrology, Vol. 146, pp. 1-9 (2003), Germany
58.
C. Micheletti, V. De Filippis, A. Maritan and F. Seno
Elucidation of the disulfide-folding pathway of hirudin by a topology based approach
Proteins: Structure, Function and Genetics, Vol.53, pp.720-730 (2003), USA
59.
A. Trovato and F. Seno
A new perspective on analysis of helix-helix packin preferences in globular proteins
Proteins: Structure, Function and Genetics, Vol.55, pp.1014-1022 (2004), USA
60.
T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar and A. Maritan
Geometry and simmetry presculpt the free-energy landscape of proteins
Proceedings of the National Academy of Science (USA), Vol. 101, pp. 7960-7964 (2004),
USA
61.
D. Marenduzzo, A. Maritan, A. Rosa and F. Seno
Stepwise unfolding of collapsed polymers
Eur. Phys. J. E 15, pp. 83-93 (2004), Germany
62.
J.R. Banavar, T.X. Hoang, A. Maritan, F. Seno and A. Trovato
Unified perspective on proteins: A physics approach
Physical Review E70, art. N. 041905 (2004), USA
63.
Y. Kapri, S.M. Bhattacharjee and F. Seno
Complete phase diagram diagram of DNA unzipping: Eye,Y fork, and triple point code
Phys. Rev. Lett., 93, art. no248102, (2004), USA
64.
T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar and A. Maritan
Geometrical model for the native state folds of proteins
Biophysical Chemistry 115, pp. 289-294 (2005), Holland
65.
A. Trovato, T.X. Hoang, J.R. Banavar, A. Maritan and F. Seno
What determines the structure s of native folds of proteins?
J. Phys. C 17, pp. S1515-S1522 (2005), UK
66.
D. Marenduzzo, T.X. Hoang, F. Seno, M. Vendruscolo and A. Maritan
On the form of growing strings
Phys. Rev. Lett 95, Art. no. 098103 (2005), USA
67.
J.R. Banavar, M. Cieplak, A. Flammini, T.X. Hoang, R.D. Kamien, T. Lezon, D.
Marenduzzo, A. Maritan, F. Seno, Y. Snir and A. Trovato
Geometry of proteins: Hydrogen bonding, sterics and marginally compact tubes
Phys. Rev. E73 , Art. No031921 (2006), USA
68.
T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar and A. Maritan
Marginal compactness of protein native structures
Phys. C18, S297-S306 (2006), UK
69.
T.X. Hoang, L. Marsella, A. Trovato, F. Seno, J.R. Banavar and A. Maritan
20
Common attributes of Native State Structures of Proteins, Disordered Proteins and Amyloid
Proceeding of the National Academy of Science USA 103, 6883-6888 (2006), USA
70.
A. Trovato, F. Chiti, A. Maritan and F. Seno
Insight into the structure of Amyloid fibrils from the Analysis of Globular Proteins
Plos Computational Biology 12, 1608-1618 (2006), USA
71.
A. Bhattacharyay, A. Trovato and F. Seno
Simple solvation potential for coarse-grained models of proteins
Proteins: Function Structure and Bioinformatics 67, 285-292 (2007), USA
72.
A. Trovato, A. Maritan and F. Seno
Aggregation of natively folded proteins: a theoretical approach
Journal of Physics Condensed matter 19, Art. N. 285221 (2007), UK
73.
F. Seno and A. Trovato
Minireview: The compact phase in polymers and proteins
Physica A 384, 122-127 (2007), Holland
74.
A. Trovato, F. Seno and S.C.E. Tosatto
The PASTA server for protein aggregation prediction
Protein Engineering Design and Selection 20, 521-523 (2007), UK
75.
F. Seno, A. Trovato, J.R. Banavar and A. Maritan
Maximum entropy approach for deducing amino acid interactions in proteins
Phys. Rev. Lett. 100, Art. No. 078102 (2008), USA
76.
T.X. Hoang, F. Seno, A. Trovato, J.R. Banavar and A. Maritan
Inference of the solvation Energy parameters of amino acids using maximum entropy
approach
J. Chem. Phys. 129, Art. No. 035102 I (2008), USA
77.
D. Marenduzzo, A. Maritan, E. Orlandini, F. Seno and A. Trovato
Phase diagrams for DNA under stretching forces
J. Stat. Mech: Theory and Experiment. Art. L04001 (2009)
78.
L. Marsella, F. Scirocco, A. Trovato , F. Seno and S.C.E. Tosatto
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by
discrete Fourier Transform
Bioinformatics 25, I289-I285 (2009) USA
79.
S. Alberghini, E. Pollone, V. Corich,M. Carlot, F. Seno, A. Trovato and A. Squartini
Consequences of relative cellular positioning on quorum sensing and bacterial cell-to-cell
communication
FEMS Microbiology Letters 292, 149-161 (2009) USA
80.
L. Cendron Trovato, F. Seno, C. Folli, B. Alfieri, G. Canotti and R. Berni
21
Amyloidogenic Potential of Transthyretin Variants INSIGHTS FROM STRUCTURAL
AND COMPUTATIONAL ANALYSES
Journal of Biological Chemistry, 284, 25832-25841 (2009), USA
81.
D. Marenduzzo, E. Orlandini, F. Seno and A. Trovato
Different pulling modes in DNA overstretching: a theoretical analysis
Phys. Rev. E81, Art. N. 051926 (2010), USA
82.
J. Maji, S.M. Bhattacharjee, F. Seno and A. Trovato
When a DNA triple helix melts: an analogue of the Efimov state
New Journal of Physics 12, Art. No. 083057 (2010), UK
83.
P. Cossio, A. Trovato, F. Pietrucci, A. Maritan, F. Seno and A. Laio
Exploring the universe of protein folds: beyond the protein data bank
Plos Computational Biology 11 , e1000957 (2010), USA
M. Baiesi, F. Seno and A. Trovato
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for
growth polarity
Proteins: Function Structure and Bioinformatics 79, 3067 (2011), USA
84.
85.
P. Cossio, D. Granata, A. Laio, F. Seno, A. Trovato
A simple and efficient statistical potential for scoring ensembles of proteins structure
Scientific Reports 2, Art. No. 351 (2012), UK
86.
J.R. Banavar, T.X. Hoang, F. Seno, A. Trovato and A.Maritan
Protein sequenze and structure:is one more foundamental than the other?
J. Stat. Physics 148, 635 (2012), USA
87.
T.X. Hoang, A. Trovato, F. Seno, J.R Banavar
Sequence repeats and protein structure
Physical Review E 86, Art. No. 050901 (2012), USA
88.
G. Kaniadakis, A. Scarfone and F. Seno
New trends in modern statistical physics
Cent. Eur. . J. of Phys. 10, 539 (2012), Germany
89.
E. Sarti, S. Zamuner, P. Cossio, A. Laio, F. Seno and A. Trovato
BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of
protein structures
Computer Physics Communications 184, 2860 (2013), Holland
90.
J. Maji, S.M. Bhattacharjee, F. Seno and A. Trovato
Melting behavior and different bound states in three-stranded DNA models
Phys. Rev. E 89, Art. No. 012121 (2014), USA
91.
A. Trovato, F. Seno, M. Zanardo, S. Alberghini, A. Tondello a nd A. Squartini
Quorum vs. diffusion sensing: a quantitative analysis of the relevance of absorbing or
reflecting boundaries
FEMS Microbiol. Lett. 352, 198 (2014), UK
22
92.
I. Walsh, F. Seno, A. Trovato and S.C.E. Tosatto
PASTA 2.0: an improved server for protein aggregation prediction.
Nucleic acids research 42 , W301-7 (2014)
93.
E. Sarti, D. Granata, Flavio Seno, A. Trovato and A. Laio
Native fold and docking pose discrimination by the same residue-based scoring function.
Proteins: Structure, Function and Bioinformatics 83, 621 (2015) , USA
94.
S. Zamuner, A. Rodriguez, F. Seno, A. Trovato
An efficient algorithm to perform local concerted movements of a chain
Plos One 10, e0118342 (2015), USA
Padova, 15 giugno 2015
Flavio Seno
23