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Abstract (12)
Journal Article (16)
Proceedings (2)
Reference Type Reference Title Journal Author Citation Progress Report Year (Date Added to Report) Document Sources
Abstract Structure Prediction of Loops with Fixed and Flexible Stems JOURNAL OF PHYSICAL CHEMISTRY B Aubramani A, Floutas C 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)
Abstract Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples JOURNAL OF CLINICAL PERIODONTOLOGY Baliban R, Sakellari D, Li Z, DiMaggio P, Garcia B, Floudas C 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)
Abstract PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization JOURNAL OF PROTEOME RESEARCH Baliban R, DiMaggio P, Plazas-Mayorca M, Garcia B, Floudas C 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)
Abstract 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 Bellows M, Floudas C 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)
Abstract De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation JOURNAL OF MEDICINAL CHEMISTRY Bellows-Peterson M, Fung H, Floudas C, Kieslich C, Zhang L, Morikis D, Wareham K, Monk P, Hawksworth O, Woodruff T 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)
Abstract A New Generation of Potent Complement Inhibitors of the Compstatin Family CHEMICAL BIOLOGY & DRUG DESIGN Lopez de Victoria A, Gorham R, Bellows-Peterson M, Ling J, Lo D, Floudas C, Monrikis D 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)
Abstract Metabolic Flux Determination in Perfed Livers by Mass Balance Analysis: Effect of Fasting BIOTECHNOLOGY AND BIOENGINEERING Orman M, Aria K, Yarmh M, Androulakis I, Berthiaume F, Ierapetritou M 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)
Abstract Pathway analysis of liver metabolism under stressed condition JOURNAL OF THEORETICAL BIOLOGY Orman M, Berthiaume F, Androulakis I, Ierapetritou M 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)
Abstract Towards accurate residue–residue hydrophobic contact prediction for α helical proteins via integer linear optimization PROTEINS Rajgaria R, McAllister S, Floudas C 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)
Abstract Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules JOVE-JOURNAL OF VISUALIZED EXPERIMENTS Smadbeck J, Peterson M, Kjoury H, Taylor M, Floudas C 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)
Abstract ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction AICHE JOURNAL Subramani A, Wei Y, Floudas C 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)
Abstract Enhanced inter-helical residue contact prediction in transmembrane proteins CHEMICAL ENGINEERING SCIENCE Wei Y, Floudas C 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)
Journal Article Novel Microtubule Polymerization Inhibitor with Potent Antiproliferative and Antitumor Activity CANCER RESEARCH Arora S, Wang X, Keenan S, Andaya C, Zhang Q, Peng Y, Welsh W 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)
Journal Article 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 Bellows M, Floutas C 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)
Journal Article A kriging based method for the solution of mixed-integer nonlinear programs containing black-box functions JOURNAL OF GLOBAL OPTIMIZATION Davis E, Ierapetritou M 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)
Journal Article A physiological model for autonomic heart rate regulation in human endotoxemia SHOCK Foteinou P, Calvano S, Lowry S, Androulakis I 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)
Journal Article Derivation of ligands for the complement C3a receptor from the C-termin of C5a EUROPEAN JOURNAL OF PHARMACOLOGY Halai R, Bellows-Peterson M, Branchett W, Smadbeck J, Kieslich C, Croker D, Cooper M, Morikis D, Woodruff T, Floudas C, Monk P 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)
Journal Article Hybrid Scoring and Classification Approaches to Predict Human Pregnane X Receptor Activators PHARMACEUTICAL RESEARCH Kortagere S, Chekmarev D, Welsh W, Ekins S 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)
Journal Article Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum JOURNAL OF CHEMICAL INFORMATION AND MODELING Kortagere S, Welsh W, Morrisey J, Daly T, Ejigiri I, Sinnis P, Vaidya A, Bergman L 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)
Journal Article Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket NUCLEIC ACIDS RESEARCH Li C, Ai N, Dinh G, Welsh W, Chen J 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)
Journal Article The Major Human Pregnane X Receptor PXR Splice Variant, PXR.2, Exhibits Significantly Diminished Ligand-Activated Transcriptional Regulation None Lin Y, Yassuda K, Assem M, Cline C, Barber J, Li C, Kholodovych V, Ai N, Chen J, Welsh W, Ekins S, Schuetz E 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)
Journal Article α-helical topology prediction and generation of distance restraints in membrane proteins. None McAllister SR, Floudas CA 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)
Journal Article Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures BMC BIOINFORMATICS Nguyen T, Almon R, DuBOis D, Jko W, Androulakis I 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)
Journal Article Metabolic flux determination in perfused livers by mass balance analysis: Effect of fasting BIOTECHNOLOGY AND BIOENGINEERING Orman M, Arai K, Yarmush M, Androulakis I, Berthiaume F, Ierapetritou M 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)
Journal Article Model building using bi-level optimization JOURNAL OF GLOBAL OPTIMIZATION Saharidis G, Androulakis I, Ierapetritou M 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)
Journal Article A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. JOURNAL OF THEORETICAL BIOLOGY Stamatelos S, Androulakis I, Kong A, Georgopoulos P 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)
Journal Article Selecting High Quality Protein Structures from Diverse Conformational Ensembles BIOPHYSICAL JOURNAL Subramani A, DiMaggio P, Floudas C 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)
Journal Article Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli MOLECULAR SYSTEMS BIOLOGY Yuan J, Doucette C, Fowler W, Feng X, Piazza M, Rabitz H, Wingreen N, Rabinowitz J 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)
Proceedings A New De Novo Approach for Optimizing Peptides that Inhibit HIV-1 Entry 17TH EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING Fung H, Floudas C, Taylor M, Siliciano R 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)
Proceedings Alpha-helical topology and tertiary structure prediction in globular proteins PROCEEDINGS OF THE 46TH IEEE CONFERENCE ON DECISION AND CONTROL, VOLS 1-14 McAlister S, Floudas C 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)

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