francesca Spyrakis
francesca Spyrakis
Unknown affiliation
Verified email at unipr.it
TitleCited byYear
Target flexibility: an emerging consideration in drug discovery and design
P Cozzini, GE Kellogg, F Spyrakis, DJ Abraham, G Costantino, A Emerson, ...
Journal of medicinal chemistry 51 (20), 6237-6255, 2008
2702008
Simple, intuitive calculations of free energy of binding for protein− ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes
M Fornabaio, F Spyrakis, A Mozzarelli, P Cozzini, DJ Abraham, ...
Journal of medicinal chemistry 47 (18), 4507-4516, 2004
1192004
Mapping the energetics of water–protein and water–ligand interactions with the “natural” HINT forcefield: predictive tools for characterizing the roles of water in biomolecules
A Amadasi, F Spyrakis, P Cozzini, DJ Abraham, GE Kellogg, A Mozzarelli
Journal of molecular biology 358 (1), 289-309, 2006
872006
Robust classification of “relevant” water molecules in putative protein binding sites
A Amadasi, JA Surface, F Spyrakis, P Cozzini, A Mozzarelli, GE Kellogg
Journal of medicinal chemistry 51 (4), 1063-1067, 2008
842008
Protein flexibility and ligand recognition: challenges for molecular modeling
F Spyrakis, A BidonChanal, X Barril, F Javier Luque
Current topics in medicinal chemistry 11 (2), 192-210, 2011
762011
Design of O-Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature
E Salsi, AS Bayden, F Spyrakis, A Amadasi, B Campanini, S Bettati, ...
Journal of medicinal chemistry 53 (1), 345-356, 2009
662009
Energetics of the protein-DNA-water interaction
F Spyrakis, P Cozzini, C Bertoli, A Marabotti, GE Kellogg, A Mozzarelli
BMC structural biology 7 (1), 4, 2007
592007
The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities
S Bruno, S Faggiano, F Spyrakis, A Mozzarelli, S Abbruzzetti, E Grandi, ...
Journal of the American Chemical Society 129 (10), 2880-2889, 2007
582007
Open challenges in structure-based virtual screening: receptor modeling, target flexibility consideration and active site water molecules description
F Spyrakis, CN Cavasotto
Archives of biochemistry and biophysics 583, 105-119, 2015
502015
Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif
MH Ahmed, F Spyrakis, P Cozzini, PK Tripathi, A Mozzarelli, JN Scarsdale, ...
PloS one 6 (9), e24712, 2011
502011
Ligand migration through the internal hydrophobic cavities in human neuroglobin
S Abbruzzetti, S Faggiano, S Bruno, F Spyrakis, A Mozzarelli, S Dewilde, ...
Proceedings of the National Academy of Sciences 106 (45), 18984-18989, 2009
492009
The consequences of scoring docked ligand conformations using free energy correlations
F Spyrakis, A Amadasi, M Fornabaio, DJ Abraham, A Mozzarelli, ...
European journal of medicinal chemistry 42 (7), 921-933, 2007
492007
Energy‐based prediction of amino acid‐nucleotide base recognition
A Marabotti, F Spyrakis, A Facchiano, P Cozzini, S Alberti, GE Kellogg, ...
Journal of computational chemistry 29 (12), 1955-1969, 2008
442008
The roles of water in the protein matrix: a largely untapped resource for drug discovery
F Spyrakis, MH Ahmed, AS Bayden, P Cozzini, A Mozzarelli, GE Kellogg
Journal of medicinal chemistry 60 (16), 6781-6827, 2017
402017
Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target
F Spyrakis, R Singh, P Cozzini, B Campanini, E Salsi, P Felici, S Raboni, ...
PloS one 8 (10), e77558, 2013
392013
The multifaceted pyridoxal 5′-phosphate-dependent O-acetylserine sulfhydrylase
A Mozzarelli, S Bettati, B Campanini, E Salsi, S Raboni, R Singh, ...
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1814 (11), 1497-1510, 2011
362011
A novel Bim-BH3-derived Bcl-XL inhibitor: biochemical characterization, in vitro, in vivo and ex-vivo anti-leukemic activity
R Ponassi, B Biasotti, V Tomati, S Bruno, A Poggi, D Malacarne, G Cimoli, ...
Cell cycle 7 (20), 3211-3224, 2008
362008
Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets
S Sottini, S Abbruzzetti, F Spyrakis, S Bettati, L Ronda, A Mozzarelli, ...
Journal of the American Chemical Society 127 (49), 17427-17432, 2005
322005
Getting it right: modeling of pH, solvent and “nearly” everything else in virtual screening of biological targets
GE Kellogg, M Fornabaio, F Spyrakis, A Lodola, P Cozzini, A Mozzarelli, ...
Journal of Molecular Graphics and Modelling 22 (6), 479-486, 2004
322004
A pipeline to enhance ligand virtual screening: integrating molecular dynamics and fingerprints for ligand and proteins
F Spyrakis, P Benedetti, S Decherchi, W Rocchia, A Cavalli, S Alcaro, ...
Journal of chemical information and modeling 55 (10), 2256-2274, 2015
312015
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