List of works - Christodoulos Floudas

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization

scientific article

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: II. Probabilistic Guarantees on Constraint Satisfaction ⬇️

scientific article published on April 16, 2012

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: III. Improving the Quality of Robust Solutions

scientific article

A Framework for Globally Optimizing Mixed-Integer Signomial Programs

scientific article published on 10 September 2013

A Mixed-Integer Optimization Framework for De Novo Peptide Identification.

scientific article published on January 2007

A New Generation of Potent Complement Inhibitors of the Compstatin Family ⬇️

scientific article published on April 26, 2011

A generalization of classical αBB underestimation to include bilinear terms

scientific article published in 2012

A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry

scientific article published on 7 March 2008

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

scientific article published on 07 August 2009

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.

scientific article

A novel clustering approach and prediction of optimal number of clusters: global optimum search with enhanced positioning

A novel clustering approach: Global optimum search with enhanced positioning

A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression

scientific article

ANTIGONE: Algorithms for coNTinuous / Integer Global Optimization of Nonlinear Equations

scientific article published on 20 March 2014

APOGEE: Global optimization of standard, generalized, and extended pooling problems via linear and logarithmic partitioning schemes

scientific article published in May 2011

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

scientific article published in February 2005

Alpha-helical topology prediction and generation of distance restraints in membrane proteins.

scientific article

An improved hybrid global optimization method for protein tertiary structure prediction

scientific article

Analysis and design of metabolic reaction networks via mixed-integer linear optimization

article by Vassily Hatzimanikatis et al published May 1996 in AIChE Journal

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies

scientific article

Big Data Approach to Batch Process Monitoring: Simultaneous Fault Detection and Diagnosis Using Nonlinear Support Vector Machine-based Feature Selection

COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.

scientific article

Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a.

scientific article published on 28 January 2010

Computational Comparison of Piecewise−Linear Relaxations for Pooling Problems

scientific article published on 17 June 2009

Computational characterization of zeolite porous networks: an automated approach

scientific article

Computational design of the lasso peptide antibiotic microcin J25 ⬇️

scientific article published on November 23, 2010

Continuous-time modeling and global optimization approach for scheduling of crude oil operations

scientific article published on 4 May 2011

Cost-effective CO2 capture based on in silico screening of zeolites and process optimization

scientific article published on 01 October 2013

De novo design and experimental characterization of ultrashort self-associating peptides

scientific article

De novo peptide design and experimental validation of histone methyltransferase inhibitors

scientific article

De novo peptide design and experimental validation of histone methyltransferase inhibitors

scientific article published in PLoS ONE

De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation

scientific article

De novo peptide identification via tandem mass spectrometry and integer linear optimization

scientific article published on February 2007

Derivation of ligands for the complement C3a receptor from the C-terminus of C5a

scientific article

Descriptor-free molecular discovery in large libraries by adaptive substituent reordering

scientific article

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

scientific article

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 ⬇️

scientific article published on November 29, 2012

Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signalling.

scientific article

Dynamically generated cutting planes for mixed-integer quadratically constrained quadratic programs and their incorporation into GloMIQO 2

scientific article published on 21 May 2014

Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5.

scientific article

Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4.

scientific article

Energy supply chain optimization of hybrid feedstock processes: a review

scientific article published on 12 March 2014

Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space

scientific article

Enhanced Continuous-Time Unit-Specific Event-Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies

Estimation of diffusion anisotropy in microporous crystalline materials and optimization of crystal orientation in membranes

scientific article published on 01 September 2013

Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning

scientific article published on August 2007

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.

scientific article

Forcefield_PTM:Ab InitioCharge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications

scientific article (publication date: 10 December 2013)

GloMIQO: Global mixed-integer quadratic optimizer

scientific article published on 7 March 2012

Global Optimization and Parametric Analysis of Large-Scale Extended Pooling Problems

scientific article published in 2010

Global Optimization of Gas Lifting Operations: A Comparative Study of Piecewise Linear Formulations

scientific article published in July 2009

Global Optimization of Large-Scale Generalized Pooling Problems: Quadratically Constrained MINLP Models

scientific article published on 2 June 2010

Global optimization advances in Mixed-Integer Nonlinear Programming, MINLP, and Constrained Derivative-Free Optimization, CDFO

scientific article published in August 2016

Global optimization of a MINLP process synthesis model for thermochemical based conversion of hybrid coal, biomass, and natural gas to liquid fuels

scientific article published in July 2012

Global optimization of mixed-integer quadratically-constrained quadratic programs (MIQCQP) through piecewise-linear and edge-concave relaxations

scientific article published on 24 May 2012

High throughput characterization of combinatorial histone codes

scientific article published on 04 August 2009

Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

scientific article published on 9 February 2016

Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models

Integrated Computational and Experimental Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity

article

Mathematical modeling and global optimization of large-scale extended pooling problems with the (EPA) complex emissions constraints

scientific article published in September 2010

Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures

scientific article

Molecular dynamics in drug design: new generations of compstatin analogs.

scientific article published on 9 February 2012

Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop

scientific article

Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop

scientific article

Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework

scientific article

New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics

scientific article

Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures.

scientific article published on 15 August 2013

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples.

scientific article published on 10 November 2011

Optimal Design of Energy Systems Using Constrained Grey-Box Multi-Objective Optimization

scientific article published on 21 February 2018

PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization.

scientific article

Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization

scientific article published in February 2004

Predictive framework for shape-selective separations in three-dimensional zeolites and metal-organic frameworks.

scientific article published on 26 April 2013

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

scientific article

Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.

scientific article

Protein WISDOM: a workbench for in silico de novo design of biomolecules

scientific article published on 25 July 2013

Protein folding and de novo protein design for biotechnological applications

scientific article

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.

scientific article

Proteomic Interrogation of Human Chromatin ⬇️

scientific article published on September 14, 2011

Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review

scientific article

Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface

scientific article

Scheduling of crude oil operations under demand uncertainty: A robust optimization framework coupled with global optimization

scientific article published on 28 October 2011

Selecting high quality protein structures from diverse conformational ensembles.

scientific article

Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations

scientific article

Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization ⬇️

scientific article published on December 13, 2011

Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data

scientific article

Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2.

scientific article

WeFold: a coopetition for protein structure prediction

scientific article

conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure

scientific article

β-sheet Topology Prediction with High Precision and Recall for β and Mixed α/β Proteins ⬇️

scientific article published on March 9, 2012

List of works by Christodoulos Floudas

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: II. Probabilistic Guarantees on Constraint Satisfaction ⬇️

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: III. Improving the Quality of Robust Solutions

A Framework for Globally Optimizing Mixed-Integer Signomial Programs

A Mixed-Integer Optimization Framework for De Novo Peptide Identification.

A New Generation of Potent Complement Inhibitors of the Compstatin Family ⬇️

A generalization of classical αBB underestimation to include bilinear terms

A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry

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

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.

A novel clustering approach and prediction of optimal number of clusters: global optimum search with enhanced positioning

A novel clustering approach: Global optimum search with enhanced positioning

A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression

ANTIGONE: Algorithms for coNTinuous / Integer Global Optimization of Nonlinear Equations

APOGEE: Global optimization of standard, generalized, and extended pooling problems via linear and logarithmic partitioning schemes

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

Alpha-helical topology prediction and generation of distance restraints in membrane proteins.

An improved hybrid global optimization method for protein tertiary structure prediction

Analysis and design of metabolic reaction networks via mixed-integer linear optimization

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies

Big Data Approach to Batch Process Monitoring: Simultaneous Fault Detection and Diagnosis Using Nonlinear Support Vector Machine-based Feature Selection

COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.

Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a.

Computational Comparison of Piecewise−Linear Relaxations for Pooling Problems

Computational characterization of zeolite porous networks: an automated approach

Computational design of the lasso peptide antibiotic microcin J25 ⬇️

Continuous-time modeling and global optimization approach for scheduling of crude oil operations

Cost-effective CO2 capture based on in silico screening of zeolites and process optimization

De novo design and experimental characterization of ultrashort self-associating peptides

De novo peptide design and experimental validation of histone methyltransferase inhibitors

De novo peptide design and experimental validation of histone methyltransferase inhibitors

De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation

De novo peptide identification via tandem mass spectrometry and integer linear optimization

Derivation of ligands for the complement C3a receptor from the C-terminus of C5a

Descriptor-free molecular discovery in large libraries by adaptive substituent reordering

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

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 ⬇️

Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signalling.

Dynamically generated cutting planes for mixed-integer quadratically constrained quadratic programs and their incorporation into GloMIQO 2

Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5.

Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4.

Energy supply chain optimization of hybrid feedstock processes: a review

Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space

Enhanced Continuous-Time Unit-Specific Event-Based Formulation for Short-Term Scheduling of Multipurpose Batch Processes: Resource Constraints and Mixed Storage Policies

Estimation of diffusion anisotropy in microporous crystalline materials and optimization of crystal orientation in membranes

Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning

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.

Forcefield_PTM:Ab InitioCharge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications

GloMIQO: Global mixed-integer quadratic optimizer

Global Optimization and Parametric Analysis of Large-Scale Extended Pooling Problems

Global Optimization of Gas Lifting Operations: A Comparative Study of Piecewise Linear Formulations

Global Optimization of Large-Scale Generalized Pooling Problems: Quadratically Constrained MINLP Models

Global optimization advances in Mixed-Integer Nonlinear Programming, MINLP, and Constrained Derivative-Free Optimization, CDFO

Global optimization of a MINLP process synthesis model for thermochemical based conversion of hybrid coal, biomass, and natural gas to liquid fuels

Global optimization of mixed-integer quadratically-constrained quadratic programs (MIQCQP) through piecewise-linear and edge-concave relaxations

High throughput characterization of combinatorial histone codes

Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models

Integrated Computational and Experimental Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity

Mathematical modeling and global optimization of large-scale extended pooling problems with the (EPA) complex emissions constraints

Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures

Molecular dynamics in drug design: new generations of compstatin analogs.

Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop

Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop

Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework

New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics

Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures.

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples.

Optimal Design of Energy Systems Using Constrained Grey-Box Multi-Objective Optimization

PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization.

Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization

Predictive framework for shape-selective separations in three-dimensional zeolites and metal-organic frameworks.

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

Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.

Protein WISDOM: a workbench for in silico de novo design of biomolecules

Protein folding and de novo protein design for biotechnological applications

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.

Proteomic Interrogation of Human Chromatin ⬇️

Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review