Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. - Andrew J. Bordner; Gary A. Huber (J. Comput. Chem., 2003)

REVCOM: a robust Bayesian method for evolutionary rate estimation. - Andrew J. Bordner; Ruben Abagyan (Bioinform., 2005)

Predicting small ligand binding sites in proteins using backbone structure. - Andrew J. Bordner (Bioinform., 2008)

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. - Andrew J. Bordner; Andrey A. Gorin (BMC Bioinform., 2008)

Predicting protein-protein binding sites in membrane proteins. - Andrew J. Bordner (BMC Bioinform., 2009)

Kernelling Method for Identifying Near-Native Protein Decoy Structures. - Xiuping Tao; Andrew J. Bordner; Thomas C. Schulthess; Andrey A. Gorin (BIOCOMP, 2010)

Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. - Andrew J. Bordner (BMC Bioinform., 2010)

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. - Andrew J. Bordner; Hans D. Mittelmann (BMC Bioinform., 2010)

MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. - Andrew J. Bordner; Hans D. Mittelmann (BMC Bioinform., 2010)

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. - Andrew J. Bordner; Barry Zorman; Ruben Abagyan (J. Comput. Aided Mol. Des., 2011)

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. - Jerez A. Te; Maoqing Dong; Laurence J. Miller; Andrew J. Bordner (J. Comput. Aided Mol. Des., 2012)