Gabriel Monteiro da Silva

FastConformation: A Standalone ML-Based Toolkit for Modeling and Analyzing Protein Conformational Ensembles at Scale

FastConformation provides a user-friendly tool for generating and analyzing protein conformational ensembles using AlphaFold 2, enabling faster and more accessible conformational predictions than traditional methods.

Mobility of Four Structural Regions Drives Isoform-Specific Properties of Plant LPOR

The paper characterizes LPOR isoform properties across six plant species, revealing differences in Chlide affinity, oligomerization, and conformational flexibility, with four mobile regions identified via AlphaFold2.

Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms and Relative State Populations

This study uses Weighted Ensemble simulations to analyze DFG flip mechanisms in Abl1 kinase and shows how compound mutations increase free energy barriers, leading to inhibitor resistance.

Predicting Relative Populations of ProteinConformations without a Physics Engine UsingAlphaFold2

This paper uses AlphaFold2 to predict protein conformational populations and mutation effects without a physics engine, achieving over 80% accuracy on two proteins.

Covalent Docking and Molecular Dynamics Simulations Reveal the Specificity-Shifting Mutations Ala237Arg and Ala237Lys in TEM Beta-Lactamase

The paper identifies two mutations in TEM beta-lactamase that shift drug specificity through salt bridges, validated by simulations and experiments.