Sandor Vajda

Diane Joseph-McCarthy

J. Chem. Inf. Model., 2024

2022

Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

2020

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.

[BibT_eX]

[DOI]

Amanda E. Wakefield

Christine Yueh

Dmitri Beglov

Marcelo Santos Castilho

J. Chem. Inf. Model., 2020

2016

Focused grid-based resampling for protein docking and mapping.

[BibT_eX]

[DOI]

J. Comput. Chem., 2016

Accounting for pairwise distance restraints in FFT-based protein-protein docking.

[BibT_eX]

[DOI]

Bing Xia

Bioinform., 2016

2015

The Impact of Side-Chain Packing on Protein Docking Refinement.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2015

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro.

[BibT_eX]

[DOI]

J. Comput. Chem., 2015

2014

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces.

[BibT_eX]

[DOI]

Tanggis Bohnuud

PLoS Comput. Biol., 2014

Docking Server for the Identification of Heparin Binding Sites on Proteins.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach.

[BibT_eX]

[DOI]

Hanieh Mirzaei

Shahrooz Zarbafian

Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking.

[BibT_eX]

[DOI]

Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

2013

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.

[BibT_eX]

[DOI]

Bioinform., 2013

A new distributed algorithm for side-chain positioning in the process of protein docking.

[BibT_eX]

[DOI]

Proceedings of the 52nd IEEE Conference on Decision and Control, 2013

Flexible refinement of protein-ligand docking on manifolds.

[BibT_eX]

[DOI]

Proceedings of the 52nd IEEE Conference on Decision and Control, 2013

2012

FTMAP: extended protein mapping with user-selected probe molecules.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2012

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2012

FTSite: high accuracy detection of ligand binding sites on unbound protein structures.

[BibT_eX]

[DOI]

Bioinform., 2012

Application of asymmetric statistical potentials to antibody-protein docking.

[BibT_eX]

[DOI]

Bioinform., 2012

A message passing approach to Side Chain Positioning with applications in protein docking refinement.

[BibT_eX]

[DOI]

Proceedings of the 51th IEEE Conference on Decision and Control, 2012

A new approach to rigid body minimization with application to molecular docking.

[BibT_eX]

[DOI]

Hanieh Mirzaei

Dmitri Beglov

Proceedings of the 51th IEEE Conference on Decision and Control, 2012

2009

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2009

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.

[BibT_eX]

[DOI]

Bioinform., 2009

2008

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2008

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.

[BibT_eX]

[DOI]

David W. Ritchie

Bioinform., 2008

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking.

[BibT_eX]

Taner Kaya

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

2007

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.

[BibT_eX]

[DOI]

IEEE Trans. Autom. Control., 2007

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking.

[BibT_eX]

[DOI]

Proceedings of the 46th IEEE Conference on Decision and Control, 2007

2006

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.

[BibT_eX]

[DOI]

Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

2005

PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2005

A Semi-Definite programming-based Underestimation method for global optimization in molecular docking.

[BibT_eX]

[DOI]

Proceedings of the 44th IEEE IEEE Conference on Decision and Control and 8th European Control Conference Control, 2005

2004

Consensus alignment server for reliable comparative modeling with distant templates.

[BibT_eX]

[DOI]

Jahnavi C. Prasad

Carlos J. Camacho

Nucleic Acids Res., 2004

ClusPro: a fully automated algorithm for protein-protein docking.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

[BibT_eX]

[DOI]

Bioinform., 2004

2003

Improved mapping of protein binding sites.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2003

Consensus alignment for reliable framework prediction in homology modeling.

[BibT_eX]

[DOI]

Bioinform., 2003

Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

2002

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.

[BibT_eX]

[DOI]

Sheldon Dennis

J. Comput. Chem., 2002

1999

Computational problems in cell biology.

[BibT_eX]

[DOI]

Charles DeLisi

Comput. Sci. Eng., 1999

1996

Peptide docking using dynamic programming.

[BibT_eX]

[DOI]

Kamalakar Gulukota

Charles DeLisi

J. Comput. Chem., 1996

1994

Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations.

[BibT_eX]

[DOI]

Ljubomir J. Buturovic

Temple F. Smith

J. Comput. Chem., 1994

1993

Loop closure via bond scaling and relaxation.

[BibT_eX]

[DOI]

J. Comput. Chem., 1993

1987

Direct and indirect least squares methods in continuous-time parameter estimation.

[BibT_eX]

[DOI]

P. Valkó

Keith R. Godfrey

Autom., 1987

1984

An extended ode solver for sensitivity calculations.

[BibT_eX]

[DOI]

P. Valkó