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Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes

PloS one, 2010-12, Vol.5 (12), p.e14383

2010

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Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes

Proteins, structure, function, and bioinformatics, 2006-05, Vol.63 (3), p.512-526

2006

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Statistical analysis and prediction of protein-protein interfaces

Proteins, structure, function, and bioinformatics, 2005-08, Vol.60 (3), p.353-366

2005

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MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes

BMC bioinformatics, 2010-09, Vol.11 (1), p.482-482, Article 482

2010

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Predicting protein-protein binding sites in membrane proteins

BMC bioinformatics, 2009-09, Vol.10 (1), p.312-312, Article 312

Bordner, Andrew J

2009

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Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

BMC bioinformatics, 2008-05, Vol.9 (1), p.234-234, Article 234

2008

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Simulating Radiating and Magnetized Flows in Multiple Dimensions with ZEUS-MP

The Astrophysical journal. Supplement series, 2006-07, Vol.165 (1), p.188-228

2006

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Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

BMC bioinformatics, 2010-01, Vol.11 (1), p.41-41, Article 41

2010

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Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

Proteins, structure, function, and bioinformatics, 2004-11, Vol.57 (2), p.400-413

2004

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Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

BMC bioinformatics, 2010-04, Vol.11 (1), p.192-192, Article 192

Bordner, Andrew J

2010

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Predicting small ligand binding sites in proteins using backbone structure

Bioinformatics, 2008-12, Vol.24 (24), p.2865-2871

Bordner, Andrew J.

2008

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Assessing the Accuracy of SAPT(DFT) Interaction Energies by Comparison with Experimentally Derived Noble Gas Potentials and Molecular Crystal Lattice Energies

Chemphyschem, 2012-12, Vol.13 (17), p.3981-3988

Bordner, Andrew J.

2012

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A new formulation of protein evolutionary models that account for structural constraints

Molecular biology and evolution, 2014-03, Vol.31 (3), p.736-749

2014

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Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

Journal of computational chemistry, 2003-02, Vol.24 (3), p.353-367

2003

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Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation

Biochemistry (Easton), 2014-06, Vol.53 (23), p.3817-3829

2014

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REVCOM: a robust Bayesian method for evolutionary rate estimation

Bioinformatics, 2005-05, Vol.21 (10), p.2315-2321

2005

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Breaking tolerance with engineered class I antigen-presenting molecules

Proceedings of the National Academy of Sciences - PNAS, 2019-02, Vol.116 (8), p.3136-3145

2019

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Importance of Each Residue within Secretin for Receptor Binding and Biological Activity

Biochemistry (Easton), 2011-04, Vol.50 (14), p.2983-2993

2011

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Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

Journal of computer-aided molecular design, 2011-10, Vol.25 (10), p.895-911

2011

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Accurate Transferable Model for Water, n-Octanol, and n-Hexadecane Solvation Free Energies

The journal of physical chemistry. B, 2002-10, Vol.106 (42), p.11009-11015

2002

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Lactam Constraints Provide Insights into the Receptor-Bound Conformation of Secretin and Stabilize a Receptor Antagonist

Biochemistry (Easton), 2011-09, Vol.50 (38), p.8181-8192

2011

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(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol: A Potent New Neuroprotectant Which Blocks N-Methyl-D-Aspartate Responses

Journal of medicinal chemistry, 1995-08, Vol.38 (16), p.3138-3145

1995

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Protein docking using surface matching and supervised machine learning

Proteins, structure, function, and bioinformatics, 2007-08, Vol.68 (2), p.488-502

2007

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Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists

Journal of computer-aided molecular design, 2012-07, Vol.26 (7), p.835-845

2012

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Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes

Statistical analysis and prediction of protein-protein interfaces

MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes

Predicting protein-protein binding sites in membrane proteins

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

Simulating Radiating and Magnetized Flows in Multiple Dimensions with ZEUS-MP

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

Predicting small ligand binding sites in proteins using backbone structure

Assessing the Accuracy of SAPT(DFT) Interaction Energies by Comparison with Experimentally Derived Noble Gas Potentials and Molecular Crystal Lattice Energies

A new formulation of protein evolutionary models that account for structural constraints

Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation

REVCOM: a robust Bayesian method for evolutionary rate estimation

Breaking tolerance with engineered class I antigen-presenting molecules

Silent Tyrosinemia Type I Without Elevated Tyrosine or Succinylacetone Associated with Liver Cirrhosis and Hepatocellular Carcinoma

Importance of Each Residue within Secretin for Receptor Binding and Biological Activity

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

Accurate Transferable Model for Water, n-Octanol, and n-Hexadecane Solvation Free Energies

Lactam Constraints Provide Insights into the Receptor-Bound Conformation of Secretin and Stabilize a Receptor Antagonist

(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol: A Potent New Neuroprotectant Which Blocks N-Methyl-D-Aspartate Responses

Protein docking using surface matching and supervised machine learning

Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists

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