3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins [PDF]
Current Research in Structural Biology, 2021 Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery.
Claudio Catalano +3 more
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3D Interaction Homology: Computational Titration of Aspartic Acid, Glutamic Acid and Histidine Can Create pH-Tunable Hydropathic Environment Maps [PDF]
Frontiers in Molecular Biosciences, 2021 Aspartic acid, glutamic acid and histidine are ionizable residues occupying various protein environments and perform many different functions in structures. Their roles are tied to their acid/base equilibria, solvent exposure, and backbone conformations.
Noah B. Herrington +2 more
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A Combined Molecular Dynamics and Hydropathic INTeraction (HINT) Approach to Investigate Protein Flexibility: The PPARγ Case Study [PDF]
MoleculesMolecular Dynamics (MD) is a computational technique widely used to evaluate a molecular system’s thermodynamic properties and conformational behavior over time.
Federica Agosta, Pietro Cozzini
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3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins [PDF]
Frontiers in Molecular Biosciences, 2023 The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary,
Mohammed H. AL Mughram +5 more
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HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham [PDF]
Frontiers in Molecular Biosciences, 2023 A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule–molecule interaction code that produces a rich variety of complex biomolecular ...
Glen E. Kellogg +3 more
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Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins [PDF]
Journal of Structural Biology: X, 2021 Knowledge of three-dimensional protein structure is integral to most modern drug discovery efforts. Recent advancements have highlighted new techniques for 3D protein structure determination and, where structural data cannot be collected experimentally ...
Mohammed H. AL Mughram +3 more
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Three-Dimensional Interaction Homology: Deconstructing Residue–Residue and Residue–Lipid Interactions in Membrane Proteins [PDF]
MoleculesA method is described to deconstruct the network of hydropathic interactions within and between a protein’s sidechain and its environment into residue-based three-dimensional maps.
Glen E. Kellogg
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Hydropathicity-based prediction of pain-causing NaV1.7 variants [PDF]
BMC Bioinformatics, 2021 Background Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant is of major clinical importance; it
Makros N. Xenakis +10 more
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Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein [PDF]
BiomoleculesAlzheimer’s disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1−40 and Aβ1−42, other C-terminally truncated Aβ peptides, including Aβ1−38 and Aβ1 ...
Rachit Pandey, Brigita Urbanc
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Configuration interaction of hydropathic waves enables ubiquitin functionality [PDF]
Physica A: Statistical Mechanics and its Applications, 2018 11pages, 4 ...
Allan, Douglas C., Phillips, J. C.
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