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1. Cestaro A, Tosatto SCE, Fogolari F, Toppo S, Valle G CASPITA @ CASP5 Meeting: BIOCOMP 2003 - Year: 2003 Full text in a new tab Topic: Structural genomics Abstract: Missing |
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2. Fogolari F, Berrera M, Molinari H Amino acid empirical contact energy definitions for fold recognition in the space of contact maps Meeting: BIOCOMP 2003 - Year: 2003 Full text in a new tab Topic: Structural genomics Abstract: Missing |
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3. Fogolari F, Haridas H, Corazza A, Esposito G, Xodo L Molecular Models for G-quadruplexes Meeting: BITS 2009 - Year: 2009 Full text in a new tab Topic: Protein Structure and Function and Computational Proteomics Abstract: Missing |
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4. Fogolari F, Pieri L, Bortolussi L, Dovier A A statistical empirical energy function for proteins Meeting: BITS 2006 - Year: 2006 Full text in a new tab Topic: Protein structure Abstract: Missing |
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5. Fogolari F, Tosatto SCE Loop predictions using molecular mechanics/Poisson- Boltzmann solvent accessible surface area (MM/PBSA) Meeting: BITS 2004 - Year: 2004 Full text in a new tab Topic: Unspecified Abstract: In many predictive tasks accurate free energy estimation is needed. The molecular mechanics/ Poisson- Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be one of the most accurate. However, the correlation between the estimated free energy and the distance (e.g. root mean square deviation (RMSD)) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In the present paper a protocol for MM/PBSA free energy estimation is designed and tested successfully on several loop decoy sets. Further integration of MM/PBSA free energy estimator with the "colony energy" approach makes the correlation between free energy and RMSD from the native structure apparent, thus making the method both accurate and robust. |
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6. Fogolari F, Tosatto SCE, Cestaro A, Valle G, Molinari H Native loop conformation recognition by MM/PBSA energy calculation Meeting: BIOCOMP 2003 - Year: 2003 Full text in a new tab Topic: Structural genomics Abstract: Missing |