Papers+Conferences

2000
Camacho CJ, Kimura SR, DeLisi C, Vajda S.  2000.  Kinetics of Desolvation-Mediated Protein–Protein Binding. Biophysical Journal. 78(3):1094-1105. Download: PDF (150.72 KB)
1999
Camacho CJ, Weng Z, Vajda S, DeLisi C.  1999.  Free Energy Landscapes of Encounter Complexes in Protein-Protein Association. Biophysical Journal. 76(3):1166-1178. Download: PDF (497.62 KB)
DeLisi C, Vajda S.  1999.  Computational problems in cell biology. Computing in Science & Engineering. 1(3):26-32. Download: PDF (185.29 KB)
1998
Zhang C, Brower RC, Kimura SR, Weng Z, Vajda S, DeLisi C.  1998.  The waters of life. Journal of the Franklin Institute. 335(2):213-240. Download: PDF (1.59 MB)
1997
Weng Z, DeLisi C, Vajda S.  1997.  Empirical free energy calculation: Comparison to calorimetric data. Protein Science. 6(9):1976-1984. Download: PDF (975.1 KB)
1996
Sezerman U, Vajda S, DeLisi C.  1996.  Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Science. 5(7):1272-1281. Download: PDF (3.29 MB)
King B, Vajda S, DeLisi C.  1996.  Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Letters. 384(1):87-91. Download: PDF (429.51 KB)
Gulukota K, Vajda S, DeLisi C.  1996.  Peptide docking using dynamic programming. Journal of Computational Chemistry. 17(4):418-428. Download: PDF (996.56 KB)
Weng Z, Vajda S, DeLisi C.  1996.  Prediction of protein complexes using empirical free energy functions. Protein Science. 5:614–626. Download: PDF (3.56 MB)
1995
Rosenfeld R, Zheng Q, Vajda S, DeLisi C.  1995.  Flexible docking of peptides to class I major-histocompatibility-complex receptors. Genetic Analysis: Biomolecular Engineering. 12(1):1-21.
Vajda S, Weng Z, DeLisi C.  1995.  Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. "Protein Engineering, Design and Selection". 8(11):1081-1092.
Rosenfeld R, Vajda S, DeLisi C.  1995.  Flexible Docking and Design. Annual Review of Biophysics and Biomolecular Structure. 24(1):677-700. Download: PDF (601.67 KB)
1994
Vajda S, Weng Z, Rosenfeld R, DeLisi C.  1994.  Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies. Biochemistry. 33(47):13977-13988. Download: PDF (1.95 MB)
1993
Rosenfeld R, Zheng Q, Vajda S, DeLisi C.  1993.  Computing the Structure of Bound Peptides. Journal of Molecular Biology. 234(3):515-521.
Sezerman U, Vajda S, Cornette J, DeLisi C.  1993.  Toward computational determination of peptide-receptor structure. Protein Science. 2(11):1827-1843.
Zheng Q, Rosenfeld R, Vajda S, DeLisi C.  1993.  Determining protein loop conformation using scaling-relaxation techniques. Protein Science. 2(8):1242-1248.
Zheng Q, Rosenfeld R, Vajda S, DeLisi C.  1993.  Loop closure via bond scaling and relaxation. Journal of Computational Chemistry. 14(5):556-565.
1990
Vajda S, DeLisi C.  1990.  Determining minimum energy conformations of polypeptides by dynamic programming. Biopolymers. 29(14):1755-1772.
Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL.  1990.  Molecular Structure and Vaccine Design. Annual Review of Biophysics and Biophysical Chemistry. 19(1):69-82. Download: PDF (461.74 KB)