James Smadbeck, Ph.D. - Publications

Affiliations: 
Chemical and Biological Engineering Princeton University, Princeton, NJ 

21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Smadbeck J, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.8
2017 Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment. Proteins. PMID 28241391 DOI: 10.1002/prot.25274  1
2016 Kieslich CA, Smadbeck J, Khoury GA, Floudas C. conSSert: Consensus SVM model for accurate prediction of ordered secondary structure. Journal of Chemical Information and Modeling. PMID 26928531 DOI: 10.1021/acs.jcim.5b00566  1
2015 Gorham RD, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. Journal of Medicinal Chemistry. 58: 814-26. PMID 25494040 DOI: 10.1021/jm501345y  1
2015 Misener R, Smadbeck JB, Floudas CA. Dynamically generated cutting planes for mixed-integer quadratically constrained quadratic programs and their incorporation into GloMIQO 2 Optimization Methods and Software. 30: 215-249. DOI: 10.1080/10556788.2014.916287  1
2014 Halai R, Bellows-Peterson ML, Branchett W, Smadbeck J, Kieslich CA, Croker DE, Cooper MA, Morikis D, Woodruff TM, Floudas CA, Monk PN. Derivation of ligands for the complement C3a receptor from the C-terminus of C5a. European Journal of Pharmacology. 745: 176-81. PMID 25446428 DOI: 10.1016/j.ejphar.2014.10.041  1
2014 Smadbeck J, Chan KH, Khoury GA, Xue B, Robinson RC, Hauser CA, Floudas CA. De novo design and experimental characterization of ultrashort self-associating peptides. Plos Computational Biology. 10: e1003718. PMID 25010703 DOI: 10.1371/journal.pcbi.1003718  1
2014 Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. Acs Synthetic Biology. 3: 855-69. PMID 24932669 DOI: 10.1021/sb400168u  1
2014 Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA. De novo peptide design and experimental validation of histone methyltransferase inhibitors. Plos One. 9: e95535. PMID 24740276 DOI: 10.1371/journal.pone.0095535  1
2014 Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/prot.24538  1
2014 Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA. De novo peptide design and experimental validation of histone methyltransferase inhibitors. Plos One. 9: e90095. PMID 24587223 DOI: 10.1371/journal.pone.0090095  1
2014 Khoury GA, Smadbeck J, Kieslich CA, Floudas CA. Protein folding and de novo protein design for biotechnological applications. Trends in Biotechnology. 32: 99-109. PMID 24268901 DOI: 10.1016/j.tibtech.2013.10.008  1
2014 Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines. Proteins. 82: 794-814. PMID 24174311 DOI: 10.1002/prot.24459  1
2013 Khoury GA, Thompson JP, Smadbeck J, Kieslich CA, Floudas CA. Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. Journal of Chemical Theory and Computation. 9: 5653-5674. PMID 24489522 DOI: 10.1021/ct400556v  1
2013 Smadbeck J, Peterson MB, Khoury GA, Taylor MS, Floudas CA. Protein WISDOM: a workbench for in silico de novo design of biomolecules. Journal of Visualized Experiments : Jove. PMID 23912941 DOI: 10.3791/50476  1
2013 Kieslich CA, Smadbeck J, Khoury GA, Floudas CA. Novel framework for beta-sheet topology prediction using low-homology template-based constraints Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 351-352.  1
2013 Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. A novel protein structure refinement method: Blind predictions during CASP10, and an optimized protocol to maximize performance Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 424-425.  1
2013 Khoury GA, Tamamis P, Smadbeck J, Szekely Z, Sinko PJ, Floudas CA. Understanding the antagonistic mechanism of a de novo designed peptide with experimental HIV fusion inhibition via molecular simulation Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 45-46.  1
2013 Smadbeck J, Kieslich CA, Khoury GA, Floudas CA. Novel biclustering framework for tertiary contact prediction using low-homology protein templates Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 616-617.  1
2013 Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska M, Sieradzan A, Smadbeck J, et al. Wefold: A collaborative protein structure prediction experiment Computational Molecular Science and Engineering Forum 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 182-184.  1
2013 Smadbeck J, Khoury GA, Chan KH, Hauser CAE, Floudas CA. Biomaterial properties of aggregating tripeptides designed using a de novo multimeric protein design framework Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 755-756.  1
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