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From LogP to computational titration: using a natural force field to predict binding affinity of protein-ligand complexes 1-gen-2003 Cozzini, Pietro; Fornabaio, M.; Spyrakis, Francesca; Kellogg, G. E.; Mozzarelli, Andrea
Computational study of the role of bridging water molecules in the energetics of protein-ligand binding 1-gen-2004 M., Fornabaio; Cozzini, Pietro; Spyrakis, Francesca; Mozzarelli, Andrea; D. J., Abraham; G. E., Kellogg
Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. Including the Free Energy Contribution of Structural Water Molecules 1-gen-2004 Fornabaio, M; Spyrakis, Francesca; Mozzarelli, Andrea; Cozzini, Pietro; Abraham, Dj; Kellogg, G. E.
Computational titration analysis of a multiprotic HIV-1 protease-ligand complex 1-gen-2004 Spyrakis, Francesca; Fornabaio, M; Cozzini, Pietro; Mozzarelli, Andrea; Abraham, Dj; Kellogg, Ge
Getting it right. Modeling of pH, Solvent and “Nearly” Everything Else in Virtual Screening of Biological Targets 1-gen-2004 G. E., Kellogg; M., Fornabaio; Spyrakis, Francesca; Lodola, Alessio; Cozzini, Pietro; Mozzarelli, Andrea; D. J., Abraham
Understanding protein-ligand interactions and binding free energy with an empirical solvation-based model 1-gen-2005 G. E., Kellogg; M., Fornabaio; Cozzini, Pietro; Mozzarelli, Andrea; Spyrakis, Francesca; D. J., Abraham
Geminate rebinding in R state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets 1-gen-2005 Sottini, Silvia; Abbruzzetti, Stefania; Spyrakis, Francesca; Bettati, Stefano; Ronda, Luca; Mozzarelli, Andrea; Viappiani, Cristiano
Evaluating docking methods with a hydropathic scoring function 1-gen-2006 M., Fornabaio; Spyrakis, Francesca; C., Calò; A., Amadasi; A., Tripathi; Cozzini, Pietro; Mozzarelli, Andrea; G. E., Kellogg
Tools for Building a Comprehensive Modeling System for Virtual Screening under Real Biological Conditions: The Computational Titration Algorithm 1-gen-2006 G. E., Kellogg; M., Fornabaio; D. L., Chen; D. J., Abraham; Spyrakis, Francesca; Cozzini, Pietro; Mozzarelli, Andrea
Water: how to evaluate its contribution in protein-ligand interactions 1-gen-2006 Cozzini, Pietro; M., Fornabaio; Mozzarelli, Andrea; Spyrakis, Francesca; G. E. KELLOGG, D. J. ABRAHAM
Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit 1-gen-2006 Spyrakis, Francesca; Raboni, Samanta; Cozzini, Pietro; Bettati, Stefano; Mozzarelli, Andrea
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 1-gen-2006 Amadasi, A; Spyrakis, Francesca; Cozzini, Pietro; Abraham, Dj; Kellogg, Ge; Mozzarelli, Andrea
A fast empirical scoring method for docking and virtual screening 1-gen-2007 Cozzini, Pietro; Spyrakis, Francesca; A., Amadasi; Mozzarelli, Andrea; G. E., Kellogg
The Reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is Controlled by the Distal HisE7 and Internal Hydrophobic Cavities 1-gen-2007 Bruno, Stefano; Faggiano, Serena; Spyrakis, Francesca; Mozzarelli, Andrea; Abbruzzetti, Stefania; Grandi, Elena; Viappiani, Cristiano; Feis, A; Mackowiak, S; Smulevich, G; Cacciatori, E; Dominici, P.
Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana 1-gen-2007 Bruno, Stefano; Faggiano, Serena; Spyrakis, Francesca; Mozzarelli, Andrea; Elena, Cacciatori; Paola, Dominici; Elena, Grandi; Abbruzzetti, Stefania; Viappiani, Cristiano
Ligand migration in non symbiotic hemoglobin AHb1 from Arabidopsis thaliana 1-gen-2007 Abbruzzetti, S.; Grandi, E.; Bruno, S.; Faggiano, S.; Spyrakis, F.; Mozzarelli, A.; Cacciatori, E.; Dominici, P.; Viappiani, C.
The consequences of scoring docked ligand conformations using free energy correlations 1-gen-2007 Spyrakis, Francesca; Amadasi, A; Fornabaio, M; Abraham, Dj; Mozzarelli, Andrea; Kellogg, Ge; Cozzini, Pietro
Complexity in modeling and understanding protonation states: computational titration of HIV-1 protease inhibitor complexes 1-gen-2007 A., Tripathi; M., Fornabaio; Spyrakis, Francesca; Mozzarelli, Andrea; Cozzini, Pietro; Ge, Kellogg
Energetics of the protein-DNA-water interaction 1-gen-2007 Spyrakis, F; Cozzini, P; Bertoli, C; Marabotti, A; Kellogg, Ge; Mozzarelli, A.
Scoring functions for virtual screening 1-gen-2007 Spyrakis, Francesca; Kellogg, G. E.; Amadasi, A; Cozzini, Pietro
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