User profiles for Andrew L. Ferguson

Andrew L Ferguson

Associate Professor of Molecular Engineering, University of Chicago
Verified email at uchicago.edu
Cited by 7049

The value of antimicrobial peptides in the age of resistance

…, Y Apidianakis, S Bradfute, AL Ferguson… - The lancet infectious …, 2020 - thelancet.com
Accelerating growth and global expansion of antimicrobial resistance has deepened the need
for discovery of novel antimicrobial agents. Antimicrobial peptides have clear advantages …

Investigating the optimal size of anticancer nanomedicine

…, S Lezmi, WG Helferich, AL Ferguson… - Proceedings of the …, 2014 - National Acad Sciences
Nanomedicines (NMs) offer new solutions for cancer diagnosis and therapy. However,
extension of progression-free interval and overall survival time achieved by Food and Drug …

Promoting transparency and reproducibility in enhanced molecular simulations

…, D Donadio, V Drobot, B Ensing, AL Ferguson… - Nature …, 2019 - hal.science
Molecular dynamics (MD) simulations have become an important tool for characterizing
mechanisms underlying complex processes, interpreting experimental measurements, and …

[PDF][PDF] Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

AL Ferguson, JK Mann, S Omarjee, T Ndung'u… - Immunity, 2013 - cell.com
A prophylactic or therapeutic vaccine offers the best hope to curb the HIV-AIDS epidemic
gripping sub-Saharan Africa, but it remains elusive. A major challenge is the extreme viral …

Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems

…, JD Chodera, AR Dinner, AL Ferguson… - Journal of chemical …, 2020 - ACS Publications
Machine learning encompasses tools and algorithms that are now becoming popular in
almost all scientific and technological fields. This is true for molecular dynamics as well, where …

Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration

W Chen, AL Ferguson - Journal of computational chemistry, 2018 - Wiley Online Library
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers
that impede efficient sampling of configurational space by standard molecular dynamics …

Helical antimicrobial polypeptides with radial amphiphilicity

…, C Yao, LF Chen, AL Ferguson… - Proceedings of the …, 2015 - National Acad Sciences
α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that
may lead to undesired peptide interactions with blood proteins and self-aggregation due to …

Hierarchical materials from high information content macromolecular building blocks: Construction, dynamic interventions, and prediction

…, M Zhao, SA Jenekhe, SV Kalinin, AL Ferguson… - Chemical …, 2022 - ACS Publications
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature.
Because hierarchy gives rise to unique properties and functions, many have sought …

Machine learning and data science in soft materials engineering

AL Ferguson - Journal of Physics: Condensed Matter, 2017 - iopscience.iop.org
In many branches of materials science it is now routine to generate data sets of such large
size and dimensionality that conventional methods of analysis fail. Paradigms and tools from …

Systematic determination of order parameters for chain dynamics using diffusion maps

AL Ferguson, AZ Panagiotopoulos… - Proceedings of the …, 2010 - National Acad Sciences
We employ the diffusion map approach as a nonlinear dimensionality reduction technique
to extract a dynamically relevant, low-dimensional description of n-alkane chains in the ideal-…