Henriette Molinari

Prof. Henriette Molinari

orcid

Research Focus & Metrics

Academic Career Length

24Years (2003-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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28 February 2003 in BMC Bioinformatics
Verified
Journal Article
Open access
PDF file
MBMarco Berrera
Marco Berrera
HMHenriette Molinari
Henriette Molinari
FFFederico Fogolari
Federico Fogolari
Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of information available from selected protein structures, with respect to a defined reference state, according to the quasi-chemical approximation. Protein-solvent interactions are estimated from residue solvent accessibility. In the approach presented here, contact energies are derived from the potential of mean force theory, several definitions of contact are examined and their performance in fold recognition is evaluated on sets of decoy structures. The best definition of contact is tested, on a more realistic scenario, on all predictions including sidechains accepted in the CASP4 experiment. In 30 out of 35 cases the native structure is correctly recognized and best predictions are usually found among the 10 lowest energy predictions. The definition of contact based on van der Waals radii of alpha carbon and side chain heavy atoms is seen to perform better than other definitions involving only alpha carbons, only beta carbons, all heavy atoms or only backbone atoms. An important prerequisite for the applicability of the approach is that the protein structure under study should not exhibit anomalous solvent accessibility, compared to soluble proteins whose structure is deposited in the Protein Data Bank. The combined evaluation of a solvent accessibility parameter and contact energy allows for an effective gross screening of predictive models.

1 January 2016 in Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Verified
Journal Article
Closed access
MAMichael Assfalg
Michael Assfalg
LRLaura Ragona
Laura Ragona
KPKatiuscia Pagano
Katiuscia Pagano
MDMariapina D'Onofrio
Mariapina D'Onofrio
SZSerena Zanzoni
Serena Zanzoni
HMHenriette Molinari
Henriette Molinari

2 February 2005 in Proteins: Structure, Function, and Bioinformatics
Verified
Journal Article
Closed access
PDF file
FFFederico Fogolari
Federico Fogolari
EMElisabetta Moroni
Elisabetta Moroni
MWMarcin Wojciechowski
Marcin Wojciechowski
MBMaciej Baginski
Maciej Baginski
LRLaura Ragona
Laura Ragona
HMHenriette Molinari
Henriette Molinari

11 October 2019 in ACS Chemical Neuroscience
Verified
Journal Article
Closed access
STSimona Tomaselli
Simona Tomaselli
PVPietro La Vitola
Pietro La Vitola
KPKatiuscia Pagano
Katiuscia Pagano
EBEdoardo Brandi
Edoardo Brandi
GSGiulia Santamaria
Giulia Santamaria
LRLaura Ragona
Laura Ragona

15 April 2019 in The Journal of Physical Chemistry Letters
Verified
Journal Article
Closed access
KPKatiuscia Pagano
Katiuscia Pagano
MPMarco Paolino
Marco Paolino
SFStefania Fusi
Stefania Fusi
VZVinicio Zanirato
Vinicio Zanirato
CTClaudio Trapella
Claudio Trapella
MOMassimo Olivucci
Massimo Olivucci

3 November 2004 in Proteins: Structure, Function, and Bioinformatics
Verified
Journal Article
Closed access
PDF file
Laura D'AlfonsoLaura D'Alfonso
Laura D'Alfonso
MCMaddalena Collini
Maddalena Collini
LRLaura Ragona
Laura Ragona
RURaffaella Ugolini
Raffaella Ugolini
GBGiancarlo Baldini
Giancarlo Baldini
HMHenriette Molinari
Henriette Molinari