Grantee Research Project Results
Publications submitted after final report Details for Grant Number R832721
Environmental Bioinformatics and Computational Toxicology Center
RFA:
Computational Toxicology: Environmental Bioinformatics Research Center (2004)
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| Reference Type | Citation | Progress Report Year (Date Added to Report) | Document Sources |
|---|---|---|---|
| Abstract | Aubramani A, Floutas C. Structure Prediction of Loops with Fixed and Flexible Stems. JOURNAL OF PHYSICAL CHEMISTRY B 2012;116(23):6670-6682 |
R832721 (Final) (08/01/22) |
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| Abstract | Baliban R, Sakellari D, Li Z, DiMaggio P, Garcia B, Floudas C. Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. JOURNAL OF CLINICAL PERIODONTOLOGY 2012;39(3):203-212 |
R832721 (Final) (08/01/22) |
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| Abstract | Baliban R, DiMaggio P, Plazas-Mayorca M, Garcia B, Floudas C. PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization. JOURNAL OF PROTEOME RESEARCH 2012;11(9):4615-4629 |
R832721 (Final) (08/01/22) |
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| Abstract | Bellows M, Floudas C. Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Virus 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases. CURRENT DRUG TARGETS 2010;11(3):264-278 |
R832721 (Final) (07/18/23) |
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| Abstract | Bellows-Peterson M, Fung H, Floudas C, Kieslich C, Zhang L, Morikis D, Wareham K, Monk P, Hawksworth O, Woodruff T. De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation. JOURNAL OF MEDICINAL CHEMISTRY 2012;55(9):4159-4168 |
R832721 (Final) (08/01/22) |
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| Abstract | Lopez de Victoria A, Gorham R, Bellows-Peterson M, Ling J, Lo D, Floudas C, Monrikis D. A New Generation of Potent Complement Inhibitors of the Compstatin Family. CHEMICAL BIOLOGY & DRUG DESIGN 2011;77(6):431-440 |
R832721 (Final) (08/01/22) |
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| Abstract | Orman M, Aria K, Yarmh M, Androulakis I, Berthiaume F, Ierapetritou M. Metabolic Flux Determination in Perfed Livers by Mass Balance Analysis: Effect of Fasting. BIOTECHNOLOGY AND BIOENGINEERING 2010;107(5):825-835 |
R832721 (Final) (08/01/22) |
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| Abstract | Orman M, Berthiaume F, Androulakis I, Ierapetritou M. Pathway analysis of liver metabolism under stressed condition. JOURNAL OF THEORETICAL BIOLOGY 2011;272(1):131-140 |
R832721 (Final) (08/01/22) |
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| Abstract | Rajgaria R, McAllister S, Floudas C. TTowards accurate residue–residue hydrophobic contact prediction for α helical proteins via integer linear optimization. PROTEINS 2008;74(4):929-947. |
R832721 (Final) (07/18/23) |
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| Abstract | Smadbeck J, Peterson M, Kjoury H, Taylor M, Floudas C. Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS 2013;(77):e50476 |
R832721 (Final) (08/01/22) |
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| Abstract | Subramani A, Wei Y, Floudas C. ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction. AICHE JOURNAL 2012;58(5):1619-1637 |
R832721 (Final) (08/01/22) |
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| Abstract | Wei Y, Floudas C. Enhanced inter-helical residue contact prediction in transmembrane proteins. CHEMICAL ENGINEERING SCIENCE 2011;66(19):4356-4369. |
R832721 (Final) (08/01/22) |
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| Journal Article | Arora S, Wang X, Keenan S, Andaya C, Zhang Q, Peng Y, Welsh W. Novel Microtubule Polymerization Inhibitor with Potent Antiproliferative and Antitumor Activity. CANCER RESEARCH 2009;69(5):1910-1915 |
R832721 (Final) (07/18/23) |
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| Journal Article | Bellows M, Floutas C. Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Vir 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases. CURRENT DRUG TARGETS 2010;11(3):264-278. |
R832721 (Final) (08/01/22) |
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| Journal Article | Davis E, Ierapetritou M. A kriging based method for the solution of mixed-integer nonlinear programs containing black-box functions. JOURNAL OF GLOBAL OPTIMIZATION 2009;43(2-3):191-205. |
R832721 (Final) (08/01/22) |
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| Journal Article | Foteinou P, Calvano S, Lowry S, Androulakis I. A physiological model for autonomic heart rate regulation in human endotoxemia. SHOCK 2011;35(3):229-239. |
R832721 (Final) (08/01/22) |
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| Journal Article | Halai R, Bellows-Peterson M, Branchett W, Smadbeck J, Kieslich C, Croker D, Cooper M, Morikis D, Woodruff T, Floudas C, Monk P. Derivation of ligands for the complement C3a receptor from the C-termin of C5a. EUROPEAN JOURNAL OF PHARMACOLOGY 2014;745:176-181. |
R832721 (Final) (08/01/22) |
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| Journal Article | Kortagere S, Chekmarev D, Welsh W, Ekins S. Hybrid Scoring and Classification Approaches to Predict Human Pregnane X Receptor Activators. PHARMACEUTICAL RESEARCH 2008;26(4):1001-1011 |
R832721 (Final) (07/18/23) |
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| Journal Article | Kortagere S, Welsh W, Morrisey J, Daly T, Ejigiri I, Sinnis P, Vaidya A, Bergman L. Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum. JOURNAL OF CHEMICAL INFORMATION AND MODELING 2010;50(5):840-849 |
R832721 (Final) (07/18/23) |
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| Journal Article | Li C, Ai N, Dinh G, Welsh W, Chen J. Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. NUCLEIC ACIDS RESEARCH 2010;38(16):5291-5303 |
R832721 (Final) (07/18/23) |
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| Journal Article | Lin Y, Yassuda K, Assem M, Cline C, Barber J, Li C, Kholodovych V, Ai N, Chen J, Welsh W, Ekins S, Schuetz E. The Major Human Pregnane X Receptor PXR Splice Variant, PXR.2, Exhibits Significantly Diminished Ligand-Activated Transcriptional Regulation. DRUG METABOLISM AND DISPOSITION 2009;37(6):1295-1304. |
R832721 (Final) (08/01/22) |
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| Journal Article | McAllister SR, Floudas CA. α-helical topology prediction and generation of distance restraints in membrane proteins. Biophysical Journal 2008;95(11):5281-5295. |
R832721 (Final) (07/18/23) |
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| Journal Article | Nguyen T, Almon R, DuBOis D, Jko W, Androulakis I. Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver:Transcriptional dynamics and regulatory structures. BMC BIOINFORMATICS 2010;11:515. |
R832721 (Final) (08/01/22) |
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| Journal Article | Orman M, Arai K, Yarmush M, Androulakis I, Berthiaume F, Ierapetritou M. Metabolic flux determination in perfused livers by mass balance analysis: Effect of fasting. BIOTECHNOLOGY AND BIOENGINEERING 2010;107(5):825-835 |
R832721 (Final) (07/18/23) |
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| Journal Article | Saharidis G, Androulakis I, Ierapetritou M. Model building using bi-level optimization. JOURNAL OF GLOBAL OPTIMIZATION 2011;49(1):49-67. |
R832721 (Final) (08/01/22) |
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| Journal Article | Stamatelos S, Androulakis I, Kong A, Georgopoulos P. A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. JOURNAL OF THEORETICAL BIOLOGY 2013;317:244-256 |
R832721 (Final) (07/18/23) |
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| Journal Article | Subramani A, DiMaggio P, Floudas C. Selecting High Quality Protein Structures from Diverse Conformational Ensembles. BIOPHYSICAL JOURNAL 2009;97(6):1728-1736. |
R832721 (Final) (08/01/22) |
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| Journal Article | Yuan J, Doucette C, Fowler W, Feng X, Piazza M, Rabitz H, Wingreen N, Rabinowitz J. Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. MOLECULAR SYSTEMS BIOLOGY 2009;5(302). |
R832721 (Final) (08/01/22) |
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| Proceedings | Fung H, Floudas C, Taylor M, Siliciano R. A New De Novo Approach for Optimizing Peptides that Inhibit HIV-1 Entry. 17TH EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING 2017;1-6 |
R832721 (Final) (08/01/22) |
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| Proceedings | McAlister S, Floudas C. Alpha-helical topology and tertiary structure prediction in globular proteins. PROCEEDINGS OF THE 46TH IEEE CONFERENCE ON DECISION AND CONTROL, VOLS 1-14 2007;9885857:4599+ |
R832721 (Final) (08/01/22) |
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.