Biology subjects

Antolinez, S.

Publications and source records attributed to Antolinez, S..

2 recordsLinked to original sources

bioRxiv2025

All-atom MD simulations of the HPV16 capsid

Human papillomavirus (HPV) type 16, one of over 200 known genotypes, is a major cause of anogenital and oropharyngeal cancers worldwide. The L1 protein capsid - which represents the exterior shell of the virus - plays essential roles in host cell adhesion and entry, and is the major antigen used in vaccines that protect against HPV. Here we report an all-atom molecular dynamics (MD) simulation of the intact capsid in explicit solvent, a calculation comprising 16.8 million atoms. The detailed motions and emergent biophysical properties revealed by this simulation provide critical insights into capsid function and immunogenicity, establishing a new platform for rational drug design and antibody engineering.

biophysics↗

bioRxiv2023

AMBERff at scale: Multimillion-atom simulations with AMBER force fields in NAMD

All-atom molecular dynamics (MD) simulations are an essential structural biology technique with increasing application to multimillion-atom systems, including viruses and cellular machinery. Classical MD simulations rely on parameter sets, such as the AMBER family of force fields (AMBERff), to accurately describe molecular motion. Here, we present an implementation of AMBERff for use in NAMD that overcomes previous limitations to enable high-performance, massively-parallel simulations encompassing up to two billion atoms. Single-point potential energy comparisons and case studies on model systems demonstrate that the implementation produces results that are as accurate as running AMBERff in its native engine.

biophysics↗