89 citations · 415 across the 21 of their papers we have counts for
11 papers · 1 filter
Deep Learning of Protein Structural Classes: Any Evidence for an 'Urfold'?
Menuka Jaiswal, Saad Saleem, Yonghyeon Kweon +4
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the int…
Machine Learning for Classification of Protein Helix Capping Motifs
Sean Mullane, Ruoyan Chen, Sri Vaishnavi Vemulapalli +4
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid bu…
Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-mimetic, Elastin-like Fusion Protein
James D. Tang, Charles E. McAnany, Cameron Mura +1
Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and oth…
Understanding the Results of Electrostatics Calculations: Visualizing Molecular 'Isopotential' Surfaces
Cameron Mura
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the u…
The Structures, Functions, and Evolution of Sm-like Archaeal Proteins (SmAPs)
Cameron Mura
Sm proteins were discovered nearly 20 years ago as a group of small antigenic proteins ( 90-120 residues). Since then, an extensive amount of biochemical and genetic data…
Claws, Disorder, and Conformational Dynamics of the C-terminal Region of Human Desmoplakin
Charles E. McAnany, Cameron Mura
Multicellular organisms consist of cells that interact via elaborate adhesion complexes. Desmosomes are membrane-associated adhesion complexes that mechanically tether the cytoskel…
Abstractions, Algorithms and Data Structures for Structural Bioinformatics in PyCogent
Marcin Cieslik, Zygmunt Derewenda, Cameron Mura
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent…
Development & Implementation of a PyMOL 'putty' Representation
Cameron Mura
The PyMOL molecular graphics program has been modified to introduce a new 'putty' cartoon representation, akin to the 'sausage'-style representation of the MOLMOL molecular visuali…
Ten Simple Rules for Creating Biomolecular Graphics
Cameron Mura
One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet's "Biochemistry" in order to appreciate t…
An Introduction to Biomolecular Simulations and Docking
Cameron Mura, Charles E. McAnany
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at…
Molecular Dynamics of a kB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation
Cameron Mura, J. Andrew McCammon
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcriptio…