Papers+Conferences

2007
Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ.  2007.  Ensemble Modeling of Substrate Binding to Cytochromes P450:  Analysis of Catalytic Differences between CYP1A Orthologs. Biochemistry. 46(10):2640-2654. Download: PDF (1012 KB)
2005
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformations in Protein Docking. Biophysical Journal. 89(2):867-875. Download: PDF (326.16 KB)
Comeau SR, Vajda S, Camacho CJ.  2005.  Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins: Structure, Function, and Bioinformatics. 60(2):239-244. Download: PDF (245.43 KB)
Comeau SR, Camacho CJ.  2005.  Predicting oligomeric assemblies: N-mers a primer. Journal of Structural Biology. 150(3):233-244. Download: PDF (809.73 KB)
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. CAPRI Meeting.  Download: PPT (5.34 MB)
2004
Rajamani D, Thiel SC, Vajda S, Camacho CJ.  2004.  Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences. 101(31):11287-11292. Download: PDF (487.94 KB)
Comeau SR, Gatchell DW, Vajda S, Camacho CJ.  2004.  ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research. 32(Web Server):W96-W99. Download: PDF (249.72 KB)
Prasad JC, Vajda S, Camacho CJ.  2004.  Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research. 32(Web Server):W50-W54. Download: PDF (376.98 KB)
Vajda S, Camacho CJ.  2004.  Protein–protein docking: is the glass half-full or half-empty? Trends in Biotechnology. 22(3):110-116. Download: PDF (166.17 KB)
Comeau SR, Gatchell DW, Vajda S, Camacho CJ.  2004.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 20(1):45-50. Download: PDF (67.49 KB)
2003
Prasad JC, Comeau SR, Vajda S, Camacho CJ.  2003.  Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 19(13):1682-1691. Download: PDF (269.21 KB)
Camacho CJ, Gatchell DW.  2003.  Successful discrimination of protein interactions. Proteins: Structure, Function, and Genetics. 52(1):92-97. Download: PDF (147.76 KB)
2002
Camacho CJ, Vajda S.  2002.  Protein–protein association kinetics and protein docking. Current Opinion in Structural Biology. 12(1):36-40. Download: PDF (78.31 KB)
2001
Kimura SR, Brower RC, Vajda S, Camacho CJ.  2001.  Dynamical View of the Positions of Key Side Chains in Protein-Protein Recognition. Biophysical Journal. 80(2):635-642. Download: PDF (809.61 KB)
Camacho CJ, Vajda S.  2001.  Protein docking along smooth association pathways. Proceedings of the National Academy of Sciences. 98(19):10636-10641. Download: PDF (355.4 KB)
Camacho CJ, Vajda S.  2001.  Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind. Drug-Receptor Thermodynamics. :581-592.
2000
Camacho CJ, Gatchell DW, Kimura SR, Vajda S.  2000.  Scoring docked conformations generated by rigid-body protein-protein docking. Proteins: Structure, Function, and Genetics. 40(3):525-537. Download: PDF (291.33 KB)
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)
Dennis S, Camacho CJ, Vajda S.  2000.  Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins: Structure, Function, and Genetics. 38(2):176-188. Download: PDF (232.57 KB)
Dennis S, Camacho CJ, Vajda S.  2000.  Exploring potential solvation sites of proteins by multistart local minimization. Optimization in Computational Chemistry and Molecular Biology. :243-261. Download: PDF (289.95 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)