89 citations · 415 across the 21 of their papers we have counts for
21 papers
Phil Bourne (1953-2026): From Small Molecules to Big Data --- The Journey of a Multifaceted Visionary
Andreas Prlić, Cameron Mura
Born in London in 1953 and raised in Australia, Phil Bourne spent over four decades in science moving across scales: from crystal structures to the world's premier structural biolo…
A Tribute to Phil Bourne -- Scientist and Human
Cameron Mura, Emma Candelier, Lei Xie
This Special Issue of Biomolecules, commissioned in honor of Dr. Philip E. Bourne, focuses on a new field of biomolecular data science. In this brief retrospective, we consider the…
Innovations in Integrating Machine Learning and Agent-Based Modeling of Biomedical Systems
Nikita Sivakumar, Cameron Mura, Shayn M. Peirce
Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches w…
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology
Tian Cai, Li Xie, Muge Chen +6
Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental h…
A Birds-eye (Re)View of Acid-suppression Drugs, COVID-19, and the Highly Variable Literature
Cameron Mura, Saskia Preissner, Robert Preissner +1
We consider the recent surge of information on the potential benefits of acid-suppression drugs in the context of COVID-19, with an eye on the variability (and confusion) across th…
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…
Ten Quick Tips for Using a Raspberry Pi
Anthony C Fletcher, Cameron Mura
Much of biology (and, indeed, all of science) is becoming increasingly computational. We tend to think of this in regards to algorithmic approaches and software tools, as well as i…
Structural biology meets data science: Does anything change?
Cameron Mura, Eli J. Draizen, Philip E. Bourne
Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations in structural biology…
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…
An Introduction to Programming for Bioscientists: A Python-based Primer
Berk Ekmekci, Charles E. McAnany, Cameron Mura
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The…
Known Structure, Unknown Function: An Inquiry-based Undergraduate Biochemistry Laboratory Course
Cynthia Gray, Carol W. Price, Christopher T. Lee +5
Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely…
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…
PaPy: Parallel and Distributed Data-processing Pipelines in Python
Marcin Cieslik, Cameron Mura
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing…
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…