Search Results - "Bordner, Andrew"

Predicting small ligand binding sites in proteins using backbone structure by Bordner, Andrew J.

“…Motivation: Specific non-covalent binding of metal ions and ligands, such as nucleotides and cofactors, is essential for the function of many proteins…”
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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 by Bordner, Andrew J.

“…The density functional version of symmetry‐adapted perturbation theory, SAPT(DFT), is a computationally efficient method for calculating intermolecular…”
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MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes by Bordner, Andrew J, Mittelmann, Hans D

“…The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such…”
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Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes by Bordner, Andrew J

“…The binding of peptide fragments of antigens to class II MHC proteins is a crucial step in initiating a helper T cell immune response. The discovery of these…”
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Predicting protein-protein binding sites in membrane proteins by Bordner, Andrew J

“…Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their…”
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A new formulation of protein evolutionary models that account for structural constraints by Bordner, Andrew J, Mittelmann, Hans D

“…Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site…”
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Statistical analysis and prediction of protein-protein interfaces by Bordner, Andrew J., Abagyan, Ruben

“…Predicting protein–protein interfaces from a three‐dimensional structure is a key task of computational structural proteomics. In contrast to geometrically…”
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Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model by Bordner, Andrew J, Mittelmann, Hans D

“…The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally…”
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Public Protests and the Risk of Novel Coronavirus Disease Hospitalizations: A County-Level Analysis from California by Bui, Linh N., Berkowitz, Rachel L., Jilek, Wendy, Bordner, Andrew J., Azar, Kristen M. J., Pressman, Alice, Romanelli, Robert J.

“…The objective of this study was to assess the relationship between public protests and county-level, novel coronavirus disease (COVID-19) hospitalization rates…”
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Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces by Bordner, Andrew J, Gorin, Andrey A

“…Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes…”
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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 by Mielke, Clinton, Lefort, Natalie, McLean, Carrie G, Cordova, Jeanine M, Langlais, Paul R, Bordner, Andrew J, Te, Jerez A, Ozkan, S. Banu, Willis, Wayne T, Mandarino, Lawrence J

“…Proteomics techniques have revealed that lysine acetylation is abundant in mitochondrial proteins. This study was undertaken (1) to determine the relationship…”
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Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes by Bordner, Andrew J., Abagyan, Ruben

“…Since determining the crystallographic structure of all peptide‐MHC complexes is infeasible, an accurate prediction of the conformation is a critical…”
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Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design by Bordner, Andrew J

“…Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However,…”
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Breaking tolerance with engineered class I antigen-presenting molecules by Parks, Christopher A., Henning, Kalli R., Pavelko, Kevin D., Hansen, Michael J., Van Keulen, Virginia P., Reed, Brendan K., Stone, Jennifer D., Schrum, Adam G., Gil, Diana, Kranz, David M., Bordner, Andrew J., Barry, Michael A., Pease, Larry R.

“…Successful efforts to activate T cells capable of recognizing weak cancer-associated self-antigens have employed altered peptide antigens to activate T cell…”
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Silent Tyrosinemia Type I Without Elevated Tyrosine or Succinylacetone Associated with Liver Cirrhosis and Hepatocellular Carcinoma by Blackburn, Patrick R., Hickey, Raymond D., Nace, Rebecca A., Giama, Nasra H., Kraft, Daniel L., Bordner, Andrew J., Chaiteerakij, Roongruedee, McCormick, Jennifer B., Radulovic, Maja, Graham, Rondell P., Torbenson, Michael S., Tortorelli, Silvia, Scott, C. Ronald, Lindor, Noralane M., Milliner, Dawn S., Oglesbee, Devin, Al-Qabandi, Wafa'a, Grompe, Markus, Gavrilov, Dimitar K., El-Youssef, Mounif, Clark, Karl J., Atwal, Paldeep S., Roberts, Lewis R., Klee, Eric W., Ekker, Stephen C.

“…ABSTRACT Tyrosinemia type I (TYRSN1, TYR I) is caused by fumarylacetoacetate hydrolase (FAH) deficiency and affects approximately one in 100,000 individuals…”
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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 by Bordner, Andrew J., Zorman, Barry, Abagyan, Ruben

“…Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However,…”
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Importance of Each Residue within Secretin for Receptor Binding and Biological Activity by Dong, Maoqing, Le, Angela, Te, Jerez A, Pinon, Delia I, Bordner, Andrew J, Miller, Laurence J

“…Secretin is a linear 27-residue peptide hormone that stimulates pancreatic and biliary ductular bicarbonate and water secretion by acting at its family B G…”
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Lactam Constraints Provide Insights into the Receptor-Bound Conformation of Secretin and Stabilize a Receptor Antagonist by Dong, Maoqing, Te, Jerez A, Xu, Xiequn, Wang, Jinhui, Pinon, Delia I, Storjohann, Laura, Bordner, Andrew J, Miller, Laurence J

“…The natural ligands for family B G protein-coupled receptors are moderate-length linear peptides having diffuse pharmacophores. The amino-terminal regions of…”
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Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor by Gao, Fan, Harikumar, Kaleeckal G, Dong, Maoqing, Lam, Polo C-H, Sexton, Patrick M, Christopoulos, Arthur, Bordner, Andrew, Abagyan, Ruben, Miller, Laurence J

“…Oligomerization of G protein-coupled receptors has been described, but its structural basis and functional importance have been inconsistent. Here, we…”
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Protein docking using surface matching and supervised machine learning by Bordner, Andrew J., Gorin, Andrey A.

“…Computational prediction of protein complex structures through docking offers a means to gain a mechanistic understanding of protein interactions that mediate…”
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