-
Chapter and Conference Paper
Attentive Deep Canonical Correlation Analysis for Diagnosing Alzheimer’s Disease Using Multimodal Imaging Genetics
Integration of imaging genetics data provides unprecedented opportunities for revealing biological mechanisms underpinning diseases and certain phenotypes. In this paper, a new model called attentive deep cano...
-
Chapter and Conference Paper
Sparse Interpretation of Graph Convolutional Networks for Multi-modal Diagnosis of Alzheimer’s Disease
The interconnected quality of brain regions in neurological disease has immense importance for the development of biomarkers and diagnostics. While Graph Convolutional Network (GCN) methods are fundamentally c...
-
Chapter
Explaining Small Molecule Binding Specificity with Volumetric Representations of Protein Binding Sites
The binding specificity of proteins is a central organizing factor in the behavior of molecular systems. Several biochemical mechanisms, including steric hindrance and electrostatic fields, collaborate to enco...
-
Article
Open AccessPrecise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials
Geometric comparisons of binding sites and their electrostatic properties can identify subtle variations that select different binding partners and subtle similarities that accommodate similar partners. Becaus...
-
Article
Open AccessRicin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk
Ricin toxin A chain (RTA) binds to stalk P-proteins to reach the α–sarcin/ricin loop (SRL) where it cleaves a conserved adenine. Arginine residues at the RTA/RTB interface are involved in this interaction. To ...
-
Article
Open AccessAn aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility
Conformational flexibility creates errors in the comparison of protein structures. Even small changes in backbone or sidechain conformation can radically alter the shape of ligand binding cavities. These chang...
-
Article
Open AccessModeling regionalized volumetric differences in protein-ligand binding cavities
Identifying elements of protein structures that create differences in protein-ligand binding specificity is an essential method for explaining the molecular mechanisms underlying preferential binding. In some ...
-
Article
Open AccessAnalysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
Structural variations caused by a wide range of physico-chemical and biological sources directly influence the function of a protein. For enzymatic proteins, the structure and chemistry of the catalytic bindin...
-
Article
Open AccessPrediction of enzyme function based on 3D templates of evolutionarily important amino acids
Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D temp...
-
Chapter and Conference Paper
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction
Determining the function of all proteins is a recurring theme in modern biology and medicine, but the sheer number of proteins makes experimental approaches impractical. For this reason, current efforts have c...
