PubRank

Christodoulos A Floudas

Author PubWeight™ 48.77‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 High throughput characterization of combinatorial histone codes. Mol Cell Proteomics 2009 2.52
2 A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization. Ind Eng Chem Res 2011 1.98
3 Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci Rep 2011 1.92
4 A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Mol Cell Proteomics 2009 1.51
5 Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity. J Am Chem Soc 2003 1.28
6 Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 2005 1.18
7 De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal Chem 2007 1.12
8 A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Mol Cell Proteomics 2010 1.11
9 A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: II. Probabilistic Guarantees on Constraint Satisfaction. Ind Eng Chem Res 2012 1.07
10 Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics 2008 1.07
11 De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation. J Med Chem 2012 1.04
12 Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. Biophys J 2007 1.03
13 A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry. J Proteome Res 2008 0.97
14 Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics 2008 0.95
15 Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning. J Bioinform Comput Biol 2007 0.95
16 Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins 2010 0.95
17 Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. J Clin Periodontol 2011 0.95
18 Computational characterization of zeolite porous networks: an automated approach. Phys Chem Chem Phys 2011 0.94
19 Proteomic interrogation of human chromatin. PLoS One 2011 0.93
20 A new generation of potent complement inhibitors of the Compstatin family. Chem Biol Drug Des 2011 0.91
21 Molecular dynamics in drug design: new generations of compstatin analogs. Chem Biol Drug Des 2012 0.90
22 WeFold: a coopetition for protein structure prediction. Proteins 2014 0.88
23 Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin. Proteins 2011 0.88
24 A Mixed-Integer Optimization Framework for De Novo Peptide Identification. AIChE J 2007 0.88
25 Selecting high quality protein structures from diverse conformational ensembles. Biophys J 2009 0.86
26 Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophys J 2008 0.86
27 Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a. J Am Soc Mass Spectrom 2010 0.86
28 Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data. Biotechnol Bioeng 2003 0.86
29 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 Synth Biol 2014 0.85
30 Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophys J 2013 0.85
31 Protein WISDOM: a workbench for in silico de novo design of biomolecules. J Vis Exp 2013 0.84
32 Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization. Proteins 2004 0.84
33 Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014 0.84
34 Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Exp Eye Res 2013 0.83
35 A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression. Toxicol Sci 2010 0.82
36 Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. J Chem Inf Model 2011 0.82
37 β-sheet topology prediction with high precision and recall for β and mixed α/β proteins. PLoS One 2012 0.81
38 An improved hybrid global optimization method for protein tertiary structure prediction. Comput Optim Appl 2010 0.80
39 Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface. J Mol Biol 2009 0.79
40 Alpha-helical topology prediction and generation of distance restraints in membrane proteins. Biophys J 2008 0.79
41 PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization. J Proteome Res 2012 0.79
42 Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines. Proteins 2013 0.79
43 Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorg Med Chem Lett 2008 0.79
44 Computational design of the lasso peptide antibiotic microcin J25. Protein Eng Des Sel 2010 0.78
45 Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization. J Clin Periodontol 2012 0.78
46 Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review. Expert Rev Proteomics 2013 0.77
47 Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space. Optim Methods Softw 2009 0.77
48 New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2014 0.76
49 conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure. J Chem Inf Model 2016 0.76
50 De novo peptide design and experimental validation of histone methyltransferase inhibitors. PLoS One 2014 0.75
51 Cost-effective CO2 capture based on in silico screening of zeolites and process optimization. Phys Chem Chem Phys 2013 0.75
52 Energy supply chain optimization of hybrid feedstock processes: a review. Annu Rev Chem Biomol Eng 2014 0.75
53 Estimation of diffusion anisotropy in microporous crystalline materials and optimization of crystal orientation in membranes. J Chem Phys 2013 0.75
54 Predictive framework for shape-selective separations in three-dimensional zeolites and metal-organic frameworks. Langmuir 2013 0.75