Publications by authors named "A G Skillman"
Article Synopsis
- Identifying cryptic pockets in proteins can reveal hidden binding sites, offering new avenues for drug development, particularly in challenging targets such as KRAS, which was thought to be "undruggable."
- The discovery of the Switch-II cryptic pocket in the KRAS mutant has led to FDA-approved cancer treatments, highlighting the clinical relevance of these pockets.
- A novel approach using weighted ensemble molecular dynamics simulations was employed to explore these cryptic pockets in KRAS, analyzing over 400 microseconds of simulations and validating the method's ability to predict binding sites while examining the mechanics of ligand interactions.
The seventh blind test of crystal structure prediction: structure ranking methods.
Acta Crystallogr B Struct Sci Cryst Eng Mater
December 2024
Article Synopsis
- Participants from 22 research groups utilized various methods, including periodic DFT-D methods, machine learning models, and empirical force fields to assess crystal structures generated from standardized sets.
- The findings indicate that DFT-D methods generally aligned well with experimental results, while one machine learning approach showed significant promise; however, the need for more efficient research methods was emphasized due to resource consumption.
The seventh blind test of crystal structure prediction: structure generation methods.
Acta Crystallogr B Struct Sci Cryst Eng Mater
December 2024
A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern.
View Article and Find Full Text PDFNovel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we performed whole-genome sequencing of 537 of 1717 SARS-CoV-2-positive nasopharyngeal/nasal swab samples collected over a nearly 20-month period from two university populations in Wisconsin, USA.
View Article and Find Full Text PDF