Carlos J. Camacho - Publications

University of Pittsburgh, Pittsburgh, PA, United States 
General Biophysics, Biochemistry

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Ye Z, Baumgartner MP, Wingert BM, Camacho CJ. Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge. Journal of Computer-Aided Molecular Design. PMID 27573981 DOI: 10.1007/s10822-016-9941-0  1
2016 Travers TS, Harlow L, Rosas IO, Gochuico BR, Mikuls TR, Bhattacharya SK, Camacho CJ, Ascherman DP. Extensive Citrullination Promotes Immunogenicity of HSP90 through Protein Unfolding and Exposure of Cryptic Epitopes. Journal of Immunology (Baltimore, Md. : 1950). PMID 27448590 DOI: 10.4049/jimmunol.1600162  1
2016 Hain E, Camacho CJ, Koes DR. Fragment oriented molecular shapes. Journal of Molecular Graphics & Modelling. 66: 143-154. PMID 27085751 DOI: 10.1016/j.jmgm.2016.03.017  1
2016 Tejero J, Kapralov AA, Baumgartner MP, Sparacino-Watkins CE, Anthonymutu TS, Vlasova II, Camacho CJ, Gladwin MT, Bayir H, Kagan VE. Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences. Biochimica Et Biophysica Acta. PMID 26928591 DOI: 10.1016/j.bbalip.2016.02.022  1
2015 Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angewandte Chemie (International Ed. in English). PMID 26385475 DOI: 10.1002/anie.201506310  1
2015 Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. Plos One. 10: e0134697. PMID 26258606 DOI: 10.1371/journal.pone.0134697  1
2015 Baumgartner MP, Camacho CJ. Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. Journal of Chemical Information and Modeling. PMID 26222931 DOI: 10.1021/acs.jcim.5b00338  1
2015 Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function. Plos One. 10: e0133590. PMID 26222440 DOI: 10.1371/journal.pone.0133590  1
2015 Koes DR, Camacho CJ. Indexing Volumetric Shapes with Matching and Packing. Knowledge and Information Systems. 43: 157-180. PMID 26085707 DOI: 10.1007/s10115-014-0729-z  1
2015 Travers T, Shao H, Joughin BA, Lauffenburger DA, Wells A, Camacho CJ. Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function. Science Signaling. 8: ra51. PMID 26012634 DOI: 10.1126/scisignal.aaa1977  1
2015 Rahaman MM, Reinders FG, Koes D, Nguyen AT, Mutchler SM, Sparacino-Watkins C, Alvarez RA, Miller MP, Cheng D, Chen BB, Jackson EK, Camacho CJ, Straub AC. Structure Guided Chemical Modifications of Propylthiouracil Reveal Novel Small Molecule Inhibitors of Cytochrome b5 Reductase 3 that Increase Nitric Oxide Bioavailability. The Journal of Biological Chemistry. PMID 26001785 DOI: 10.1074/jbc.M114.629964  1
2015 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. Journal of Virology. 89: 4191-200. PMID 25631078 DOI: 10.1128/JVI.00157-15  1
2014 Koes DR, Camacho CJ. Shape-based virtual screening with volumetric aligned molecular shapes. Journal of Computational Chemistry. 35: 1824-34. PMID 25049193 DOI: 10.1002/jcc.23690  1
2013 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. Bioorganic & Medicinal Chemistry. 21: 7763-78. PMID 24231650 DOI: 10.1016/j.bmc.2013.10.015  1
2013 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. 14: 125-35. PMID 23954152 DOI: 10.1016/j.chom.2013.06.008  1
2013 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. The International Journal of Biochemistry & Cell Biology. 45: 1051-63. PMID 23466492 DOI: 10.1016/j.biocel.2013.02.015  1
2013 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. Biophysical Journal. 104: 705-15. PMID 23442921 DOI: 10.1016/j.bpj.2012.12.003  1
2013 Koes DR, Baumgartner MP, Camacho CJ. Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. Journal of Chemical Information and Modeling. 53: 1893-904. PMID 23379370 DOI: 10.1021/ci300604z  1
2012 Koes DR, Camacho CJ. ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Research. 40: W409-14. PMID 22553363 DOI: 10.1093/nar/gks378  1
2012 Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Research. 40: W387-92. PMID 22523085 DOI: 10.1093/nar/gks336  1
2012 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. 7: e32839. PMID 22427896 DOI: 10.1371/journal.pone.0032839  1
2012 Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics (Oxford, England). 28: 784-91. PMID 22210869 DOI: 10.1093/bioinformatics/btr717  1
2012 Huang Y, Wolf S, Koes D, Popowicz GM, Camacho CJ, Holak TA, Dömling A. Exhaustive fluorine scanning toward potent p53-Mdm2 antagonists. Chemmedchem. 7: 49-52. PMID 21954050 DOI: 10.1002/cmdc.201100428  1
2012 Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure Bioinformatics. 28: 1951. DOI: 10.1093/bioinformatics/bts305  1
2011 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, ... ... Camacho CJ, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/j.jmb.2011.09.031  1
2011 Koes DR, Camacho CJ. Pharmer: efficient and exact pharmacophore search. Journal of Chemical Information and Modeling. 51: 1307-14. PMID 21604800 DOI: 10.1021/ci200097m  1
2010 Bueno M, Temiz NA, Camacho CJ. Novel modulation factor quantifies the role of water molecules in protein interactions. Proteins. 78: 3226-34. PMID 20665475 DOI: 10.1002/prot.22805  1
2010 Meireles LM, Dömling AS, Camacho CJ. ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Research. 38: W407-11. PMID 20525787 DOI: 10.1093/nar/gkq502  1
2010 Temiz AN, Benos PV, Camacho CJ. Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Research. 38: 2134-44. PMID 20047959 DOI: 10.1093/nar/gkp1132  1
2010 Temiz NA, Trapp A, Prokopyev OA, Camacho CJ. Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting. Bioinformatics (Oxford, England). 26: 319-25. PMID 19965883 DOI: 10.1093/bioinformatics/btp664  1
2009 Liu J, Faeder JR, Camacho CJ. Toward a quantitative theory of intrinsically disordered proteins and their function. Proceedings of the National Academy of Sciences of the United States of America. 106: 19819-23. PMID 19903882 DOI: 10.1073/pnas.0907710106  1
2009 Hofmann WA, Arduini A, Nicol SM, Camacho CJ, Lessard JL, Fuller-Pace FV, de Lanerolle P. SUMOylation of nuclear actin. The Journal of Cell Biology. 186: 193-200. PMID 19635839 DOI: 10.1083/jcb.200905016  1
2009 Temiz NA, Camacho CJ. Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Research. 37: 4076-88. PMID 19429892 DOI: 10.1093/nar/gkp289  1
2008 Camacho CJ, Katsumata Y, Ascherman DP. Structural and thermodynamic approach to peptide immunogenicity. Plos Computational Biology. 4: e1000231. PMID 19023401 DOI: 10.1371/journal.pcbi.1000231  1
2008 Camacho CJ. Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation. Plos One. 3: e3342. PMID 18833322 DOI: 10.1371/journal.pone.0003342  1
2007 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 Journal of Autoimmunity. 29: 174-186. PMID 17826948 DOI: 10.1016/j.jaut.2007.07.005  1
2007 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. 69: 786-92. PMID 17803211 DOI: 10.1002/prot.21722  1
2007 Champ PC, Camacho CJ. FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Research. 35: W556-60. PMID 17537824 DOI: 10.1093/nar/gkm326  1
2007 Bueno M, Camacho CJ, Sancho J. SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles. Proteins. 68: 850-62. PMID 17523191 DOI: 10.1002/prot.21453  1
2007 Iyer AK, 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. Journal of Cellular Physiology. 211: 748-58. PMID 17311283 DOI: 10.1002/jcp.20986  1
2007 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. 46: 2640-54. PMID 17300179 DOI: 10.1021/bi062320m  1
2006 Camacho CJ, Ma H, Champ PC. Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions. Proteins. 63: 868-77. PMID 16506242 DOI: 10.1002/prot.20932  1
2005 Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins. 60: 239-44. PMID 15981265 DOI: 10.1002/prot.20564  1
2005 Camacho CJ. Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins. 60: 245-51. PMID 15981253 DOI: 10.1002/prot.20565  1
2005 Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophysical Journal. 89: 867-75. PMID 15908573 DOI: 10.1529/biophysj.104.058768  1
2005 Comeau SR, Camacho CJ. Predicting oligomeric assemblies: N-mers a primer. Journal of Structural Biology. 150: 233-44. PMID 15890272 DOI: 10.1016/j.jsb.2005.03.006  1
2005 Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics (Oxford, England). 21: 2534-6. PMID 15713734 DOI: 10.1093/bioinformatics/bti322  1
2004 Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 101: 11287-92. PMID 15269345 DOI: 10.1073/pnas.0401942101  1
2004 Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research. 32: W96-9. PMID 15215358 DOI: 10.1093/nar/gkh354  1
2004 Prasad JC, Vajda S, Camacho CJ. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research. 32: W50-4. PMID 15215349 DOI: 10.1093/nar/gkh456  1
2004 Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends in Biotechnology. 22: 110-6. PMID 15036860 DOI: 10.1016/j.tibtech.2004.01.006  1
2004 Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics (Oxford, England). 20: 45-50. PMID 14693807 DOI: 10.1093/bioinformatics/btg371  1
2003 Prasad JC, Comeau SR, Vajda S, Camacho CJ. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics (Oxford, England). 19: 1682-91. PMID 12967965 DOI: 10.1093/bioinformatics/btg211  1
2003 Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins. 52: 92-7. PMID 12784373 DOI: 10.1002/prot.10394  1
2003 Prasad JC, Silberstein M, Camacho CJ, Vajda S. Homology modeling of proteins using multiple models and consensus sequence alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2812: 389-401.  1
2002 Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Current Opinion in Structural Biology. 12: 36-40. PMID 11839487 DOI: 10.1016/S0959-440X(02)00286-5  1
2001 Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proceedings of the National Academy of Sciences of the United States of America. 98: 10636-41. PMID 11517309 DOI: 10.1073/pnas.181147798  1
2001 Kimura SR, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition Biophysical Journal. 80: 635-642. PMID 11159432  1
2000 Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Physical Review Letters. 85: 2641-4. PMID 10978127 DOI: 10.1103/PHYSREVLETT.85.2641  1
2000 Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins. 40: 525-37. PMID 10861944 DOI: 10.1002/1097-0134(20000815)40:3<525::AID-PROT190>3.0.CO;2-F  1
2000 Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophysical Journal. 78: 1094-105. PMID 10692300 DOI: 10.1016/S0006-3495(00)76668-9  1
2000 Dennis S, Camacho CJ, Vajda S. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins. 38: 176-88. PMID 10656264 DOI: 10.1002/(SICI)1097-0134(20000201)38:2<176::AID-PROT6>3.0.CO;2-O  1
1999 Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal. 76: 1166-78. PMID 10049302 DOI: 10.1016/S0006-3495(99)77281-4  1
1997 Camacho CJ, Schanke T. From collapse to freezing in random heteropolymers Europhysics Letters. 37: 603-608. DOI: 10.1209/epl/i1997-00197-2  1
1997 Bellissard J, Camacho CJ, Barelli A, Claro F. Exact random walk distributions using noncommutative geometry Journal of Physics a: Mathematical and General. 30: L707-L709. DOI: 10.1088/0305-4470/30/21/001  1
1996 Camacho CJ. Entropic Barriers, Frustration, and Order: Basic Ingredients in Protein Folding. Physical Review Letters. 77: 2324-2327. PMID 10061915  1
1996 Camacho CJ, Thirumalai D. Denaturants can accelerate folding rates in a class of globular proteins. Protein Science : a Publication of the Protein Society. 5: 1826-32. PMID 8880906 DOI: 10.1002/pro.5560050908  1
1996 Camacho CJ, Thirumalai D. A criterion that determines fast folding of proteins: A model study Europhysics Letters. 35: 627-632. DOI: 10.1209/epl/i1996-00162-1  1
1995 Camacho CJ, Thirumalai D. Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins. 22: 27-40. PMID 7675784 DOI: 10.1002/prot.340220105  1
1995 Camacho CJ, Thirumalai D. Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 92: 1277-81. PMID 7533290 DOI: 10.1073/pnas.92.5.1277  1
1993 Camacho CJ, Thirumalai D. Minimum energy compact structures of random sequences of heteropolymers. Physical Review Letters. 71: 2505-2508. PMID 10054697 DOI: 10.1103/PhysRevLett.71.2505  1
1993 Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proceedings of the National Academy of Sciences of the United States of America. 90: 6369-72. PMID 8327519 DOI: 10.1073/pnas.90.13.6369  1
1992 Camacho CJ, Fisher ME, Straley JP. Rods to self-avoiding walks to trees in two dimensions. Physical Review. A. 46: 6300-6310. PMID 9907941 DOI: 10.1103/PhysRevA.46.6300  1
1991 Camacho CJ, Fisher ME, Singh RRP. Semiflexible planar polymeric loops The Journal of Chemical Physics. 94: 5693-5700.  1
1990 Camacho CJ, Fisher ME. Tunable fractal shapes in self-avoiding polygons and planar vesicles. Physical Review Letters. 65: 9-12. PMID 10042159 DOI: 10.1103/PhysRevLett.65.9  1
1990 Maggs AC, Leibler S, Fisher ME, Camacho CJ. Size of an inflated vesicle in two dimensions. Physical Review. A. 42: 691-695. PMID 9904076 DOI: 10.1103/PhysRevA.42.691  1
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