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Protein-Protein Interactions (PPIs)

  • T. Travers, H. Shao, B. A. Joughin, D. A. Lauffenburger, A. Wells, C. J. Camacho, Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function. Sci. Signal. 2015. 8(378):
  • Shao H, Travers T, Camacho CJ, Wells A. The carboxyl tail of alpha-actinin-4 regulates its susceptibility to m-calpain and thus functions in cell migration and spreading. Int J Biochem Cell Biol. 2013 Jun;45(6):1051-63. Epub 2013 Mar 1. (PMID: 23466492).
  • Travers T, Shao H, Wells A, Camacho CJ. Modeling the assembly of the multiple domains of α-actinin-4 and its role in actin cross-linking. Biophys J. 2013 Feb 5;104(3):705-15.  (PMID: 23442921).
  • Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25;414(2):289-302. Epub 2011 Sep 29. (PMID: 22001016) 

Drug Discovery

  • Baumgartner MP and Camacho CJ. Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. J Chem Inf Model 2015. (PMID: 26222931)
  • Grover P, Haibin Shi, Baumgartner MP, Camacho CJ, and Smithgall TE. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL kinase function. PLOS ONE. 2015. 10, e0133590.  (PMID: 25376742)
  • Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE. A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region. Chem Biol Drug Des. 2014 Nov 6.  (PMID: 25376742).
  • Koes DR, Camacho CJ. Shape-based virtual screening with volumetric aligned molecular shapes. J Comput Chem. 2014 Sep 30;35(25):1824-34. Epub 2014 Jul 22.  (PMID: 25049193).
  • Wisastra R, Kok PA, Eleftheriadis N, Baumgartner MP, Camacho CJ, Haisma HJ, Dekker FJ. Discovery of a novel activator of 5-lipoxygenase from an anacardic acid derived compound collection. Bioorg Med Chem. 2013 Dec 15;21(24):7763-78. Epub 2013 Oct 23. (PMID: 24231650).
  • Koes DR, Baumgartner MP, Camacho CJ. Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. J Chem Inf Model. 2013 Aug 26;53(8):1893-904. Epub 2013 Feb 12.  (PMID: 23379370).
  • Koes DR, Camacho CJ. ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W409-14. Epub 2012 May 2. (PMID: 22553363). (
  • Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W387-92. Epub 2012 Apr 20. (PMID: 22523085). (
  • Koes D, Khoury K, Huang Y, Wang W, Bista M, Popowicz GM, Wolf S, Holak TA, Dömling A, Camacho CJ. Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One. 2012;7(3):e32839. Epub 2012 Mar 12. (PMID: 22427896). (
  • Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ. Ensemble Modeling of Substrate Binding to Cytochromes P450: Analysis of Catalytic Differences Between CYP1A Orthologs. Biochemistry. 2007 46, 2640-54. (PMID: 17300179)
  • Bueno M, Camacho CJ, Randhawa, PS. A molecular modeling approach to develop compounds with antoBK-virus activity. American Journal of Transplantation. 2008 8, 284-285.
  • Zeng G, Bueno M, Camacho CJ, Ramaswami B, Luo C, Randhawa P. Validation of BKV large T-antigen ATP-binding site as a target for drug discovery. Antiviral Res. 2009 2:184-7. (PMID: 19084558)
  • Huang Y, Wolf S, Bista M, Meireles L., Camacho CJ, Holak TA, Domling A. 1,4-Thienodiazepine-2,5-diones via MCR (I): Synthesis, Virtual Space and p53-Mdm2 Activity. Chem Biol Drug Des. 2010.
  • Meireles L., Domling A, Camacho CJ. ANCHOR: A Web Server and Database for Analysis of Protein-Protein Interaction Binding Pockets for Drug Discovery. Nucleic Acids Res. 2010.
  • Koes D, Camacho CJ.  Pharmer: Efficient and Exact Pharmacophore Search. J. Chem. Inf. Model. 2011.
  • Huang Y, Wolf S, Koes D, PopoWicz G, Camacho CJ, Holak A, Domling A.  Exhaustive Flourine Scanning toward Potent p53-Mdm2 Antagonists. ChemMedChem. 2012.
  • Koes D, Camacho CJ. Small-Molecule Inhibitor Starting Points Learned From Protein-Protein Interaction Inhibitor Structure. Bioinformatics. 2011


Disordered Proteins


Protein-DNA Interactions
  • Temiz NA, Camacho CJ. Experimentally based contact energies decode the promiscuous non-additive interactions of C2H2 zinc finger transcription factors. Nucleic Acids Res. 2009 37:4076-88
  • Temiz NA, Camacho CJ. Electrostatic hot spot on DNA binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res. 2010 38:2134-44. (PMID: 20047959)
  • Temiz NA, Trapp A, Prokopyev O, Camacho CJ. Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting. Bioinformatics. 2010 26:319-25. (PMID: 19965883).



  • Kwun HJ, Shuda M, Camacho CJ, Gamper AM, Thant M, Chang Y, Moore PS. Restricted Protein Phosphatase 2A Targeting by Merkel Cell Polyomavirus Small T Antigen. J Virol. 2015 Jan 28. pii: JVI.00157-15. (PMID: 25631078).
  • Kwun HJ, Shuda M, Feng H, Camacho CJ, Moore PS, Chang Y. Merkel cell polyomavirus small T antigen controls viral replication and oncoprotein expression by targeting the cellular ubiquitin ligase SCFFbw7. Cell Host Microbe. 2013 Aug 14;14(2):125-35.  (PMID: 23954152).
  • Katsumata Y, Ridgway WM, Oriss T, Gu X, Chin D, Wu Y, Fertig N, Oury T, Vandersteen D, Clemens P, Camacho CJ, Weinberg A, Ascherman DP. Species-specific immune responses generated by histidyl-tRNA synthetase immunization are associated with muscle and lung inflammation. J. Autoimmun. 2007 29, 174-86. (PMID: 17826948)
  • Camacho CJ, Katsumata Y, Ascherman DP. Structural and Thermodynamic Approach to Peptide Immunogenicity. PLoS Comput Biol. 2008 4, e1000231. 


Molecular Recognition

  • Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 1999 76, 1166-1178. 
  • Dennis S, Camacho CJ, Vajda S. Continuum Electrostatic Analysis of Preferred Solvation Sites around Proteins in Solution. Proteins: Structure, Function, and Genetics. 2000 38, 176-188. (PMID: 10656264)
  • Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation mediated protein-protein binding. Biophys. J. 2000 78, 1094-1105. (PMID: 10692300)
  • Kimura SR, Brower RC, Vajda S, and Camacho CJ. Dynamical view of the positions of key side chains in protein recognition. Biophys. J. 2001 80, 635-642. (PMID: 11159432)
  • Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 2004 101, 11287-92.
  • Camacho CJ. Modeling side chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins. 2005 60, 245-251. (PMID: 15981253)
  • Camacho CJ, DeLisi C, Vajda S. “Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind” in Drug-Receptor Thermodynamics, edited by R.B. Raffa, Wiley (2001) 581-592.
  • Dennis S, Camacho CJ, Vajda S. “Exploring potential solvation sites of proteins by multistart local minimization” in  Optimization in Computational Chemistry and Molecular Biology, edited by C.A. Floudas and P.M. Pardalos, Kluwer Academic Publishers (2000) 1-19.

Protein Docking

  • Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA. 2001 98, 10636-10641.
  • Camacho CJ, Vajda S. Protein-Protein association kinetics and protein docking. Curr. Opin. Struct. Biol. 2002 12, 36-40. (PMID: 11839487)
  • Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins: Structure, Function, and Genetics. 2003 52, 92-97. (PMID: 12784373)
  • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 2004 20, 45-50.
  • Vajda S, Camacho CJ. Protein-protein docking: is the glass half full or half empty? Trends Biotechnol. 2004 22, 110-116. (PMID: 15036860)
  • Comeau SR, Gatchell D, Vajda S, Camacho CJ. ClusPro: A Fully-Automated Algorithm for Protein-Protein Docking,” Nucleic Acid Res. 2004 32, W96-9. (PMID: 15215358)
  • Comeau S, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds3-5. Proteins. 2005 60, 239-244. (PMID: 15981265)
  • Comeau S, Camacho CJ. Predicting oligomeric assemblies:N-mers a primer. J. Struct. Biol. 2005 150, 233-244. (PMID: 15890272).
  • Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near native conformations in protein docking. Biophys. J. 2005 89, 867-875.


Protein Scoring Functions

  • Camacho CJ, Gatchell DW, Kimura SR, DeLisi C, Vajda S. Scoring docked conformations generated by rigid body protein-protein docking. Proteins: Structure, Function, and Genetics. 2000 40, 525-537.
  • Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics. 2005 21, 2534-2536. 
  • Camacho CJ, Ma H., Champ PC. Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. Proteins. 2006 63, 868-877. (PMID: 16506242)
  • Bueno M, Camacho CJ., Sancho J. SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles. Proteins. 2007 68, 850-62. (PMID: 17523191)
  • Champ PC, Camacho CJ. FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acid Res. 2007 35, 556-60. (PMID: 17537824)
  • Bueno M, Camacho CJ. Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI. Proteins. 2007 69, 786-92. (PMID: 17803211)
  • Bueno M, Temiz NA, Camacho CJ. Novel modulation factor quantifies the role of water molecules in protein interactions. Proteins. 2010.


Cell Biology and Ion channels

  • Iyer AKV, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. Tenascin Cytotactin Epidermal Growth Factor-Like Repeat Binds Epidermal Growth Factor Receptor with Low Affinity. J. Cell Phys. 2007 211, 748-58. (PMID: 17311283)
  • Camacho CJ. Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation. PLoS ONE 2008 3, e3342. 
  • Hofmann WA, Arduini A, Nicol SM, Camacho CJ, Lessard JL, Fuller-Pace FV, de Lanerolle P. SUMOylation of nuclear actin. J. Cell Biol. 2009 186:193-200.


Protein Folding

  • Camacho CJ, Thirumalai D. Kinetics and Thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 1993  90, 6369-6372. 
  • Camacho CJ, Thirumalai D. Minimum energy compact structures in random sequences of heteropolymers. Phys. Rev. Lett. 1993 71, 2505-2508. (PMID: 10054697)
  • Camacho CJ, Thirumalai D. Theoretical Predictions of Folding Pathways in BPTI using the Proximity Rule. Proc. Natl. Acad. Sci. USA. 1995  92, 1277-1281. 
  • Camacho CJ, Thirumalai D. Modeling the Role of Disulfide Bonds in Protein Folding: Entropic Barriers and Pathways. Proteins: Structure, Function, and Genetics. 1995 22, 27-40. (PMID: 7675784)
  • Camacho CJ. Entropic Barriers, Frustration, and Order: Basic Ingredients in Protein Folding. Phys. Rev. Lett. 1996 77, 2324-2328. (PMID: 10061915)
  • Camacho CJ, Thirumalai D. Denaturants can Accelerate Folding Rates in a Class of Globular Proteins. Protein Science. 1996 5, 1826-1832. (PMID: 8880906)
  • Camacho CJ, Thirumalai D. A Criterion that Determines Fast Folding of Proteins: a Model Study. Europhysics Letters. 1996 35, 627-632.
  • Camacho CJ. Chain Length Scaling of Protein Folding Time. Phys. Rev. Lett. 1998 80, 207.



  • Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions: Evolution by gene duplication and modification. Phys. Rev. Lett. 2000 85, 2641-2644.


Homology Modeling

  • Prasad JC, Comeau SR, Vajda S, Camacho CJ. Consensus Alignment for Reliable Framework Prediction in Homology Modeling. Bioinformatics. 2003 19, 1682-1691.
  • Prasad JC, Vajda S, Camacho CJ. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acid Res. 2004 32, W50-4. 
  • Prasad JC, Silberstein M, Camacho CJ, Vajda S. Homology modeling of proteins using multiple models and consensus sequence. Lect N Bioinformat. 2003 2812, 389-401.


Physics of Biology

  • Maggs AC,Leibler S, Fisher ME, Camacho CJ. Size of an inflated vesicle in two dimensions. Phys. Rev. A 1990 42, 691-695. (PMID: 9904076)
  • Camacho CJ, Fisher ME. Tunable fractal shapes in self-avoiding polygons and planar vesicles. Phys. Rev. Lett. 1990 65, 9-12. (PMID: 10042159)
  • Camacho CJ, Fisher ME, Singh RRP. Semiflexible planar polymeric loops. J. Chem. Phys. 1991 94, 5693-5700.
  • Camacho CJ, Fisher ME, Straley JP. Crossover from Rods to Self-avoiding Walks to Trees in Two Dimensions. Phys. Rev. A 1992 46, 6300-6310. (PMID: 9907941)
  • Camacho CJ, Schanke T. From Collapse to Freezing in Random Heteropolymers. Europhysics Letters. 1997 37, 603-608.
  • Camacho CJ, Fisher ME. “Simulations of planar vesicles and their transitions” in Computer Simulation Studies in Condensed Matter Physics IV, edited by D. P. Landau, K. K. Mon and H. B. Schuttler (1991).


Nonlinear Physics

  • Camacho CJ, F. Lund L. Generation of Boussinesq solitons via boundary conditions. Phys. Lett. A 1985 108, 1-3.
  • Camacho CJ, F. Lund L. Inelastic scattering of Toda solitons by an interface. Physica D 1987 26, 379-384.
  • Bellissard J, Camacho CJ, Barelli A, Claro F. Exact Random Walk Distributions using Noncommutative Geometries. J. Phys. A. 1997 30, L707-L709.
  • Camacho CJ, Lomnitz-Adler J, Lund F. “Approximate modelling of accelerograms: Theory and applications” in Quintas Jornadas Chilenas de Sismologia e Ingenieria Antisismica, ed. by Ministerio de Vivienda y Urbanismo, Santiago (1989) 399-404.
  • Camacho CJ, Lund F. “Generation of solitons in non-integrable systems” in Nonlinear evolution equations: Integrability and spectral methods, edited by Degasperis, Fordy and Lakshmanan, Manchester University Press (1990) 483-495.



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