Protein Structure and Dynamics

MDTAP automates the analysis of permeation events across membrane proteins and nucleic acids from MD trajectories, providing visualization and insights into solute/solvent transport mechanisms.

PPIFold automates PPI analysis using AlphaPullDown, simplifying workflows and improving accessibility for researchers.

ABCFold simplifies running and comparing AlphaFold 3, Boltz-1, and Chai-1 for protein structure prediction with standardized input and unified result handling.

Isopeptor detects intramolecular isopeptide bonds in protein structures using structure-guided template matching and logistic regression, achieving high recall and precision on a curated PDB subset.

PairK improves prediction of biologically relevant SLiM interactions by quantifying motif conservation in disordered regions more effectively than existing methods.

This study investigates how Guanidine Hydrochloride affects the structural behavior of two intrinsically disordered proteins using simulations and SAXS profiles.

drMD is an automated pipeline for running molecular dynamics simulations, designed to reduce the expertise required and improve accessibility for non-experts.

The paper investigates the structural dynamics of the C-terminal region of SARS-CoV-2 ORF6, identifying key residues like Met58 and di-acidic motifs that influence its structural conformations and functional properties.

AlphaMut uses reinforcement learning to predict helix-disrupting mutations by analyzing amino acid effects on protein structure.

The paper benchmarks protein stability models on double point mutations and finds they fail to capture epistatic interactions, with some improvements from epistasis-aware models.

The paper develops a yeast-based protein folding sensor to study indel variants, finding that most tolerated indels occur in specific regions and that computational tools can predict their effects.

The paper designs large pseudosymmetric protein nanoparticles using a hierarchical computational method, achieving sizes up to 96 nm with 960 subunits.

The paper introduces a method to design pseudosymmetric protein hetero-oligomers by redesigning symmetric homo-oligomers and recombining them to form new hetero-oligomers with high structural specificity.

This paper evaluates AlphaFold2's ability to model coiled-coil domains, showing improved prediction of oligomeric states compared to previous methods.

This study investigates how different water models affect water molecule migration through enzyme tunnels, finding that TIP3P allows faster and greater transport compared to OPC and TIP4P-Ew.

The paper uses generative models to predict absolute protein stability, achieving a mean error of 1.5 kcal/mol and a correlation coefficient of 0.7.

The paper introduces MapTurns, a web server that maps beta turn structures and side chain interactions using sequence motifs and provides tools for mutational analysis and protein design.

The paper analyzes insulin dimer dissociation using a computational framework to identify pathways and quantify their contributions to the dissociation rate.

The paper uses SAXS data and modeling to analyze the conformational ensemble of monomeric pre-fibrillar human alpha-synuclein, concluding a shifting equilibrium of curved models with low alpha-helical content.

This study determines the structure of apoB100 from human LDL using cryo-EM, AlphaFold2, and molecular dynamics, revealing its structural organization and functional domains.

The paper examines small viral proteins in cellular membranes, highlighting their structural diversity and the need for a multi-pronged approach to understand their function and conformational dynamics.

This study shows that PEG affects phase-separated droplets differently depending on the protein, accelerating Nup98 maturation but stabilizing BSA droplets.

This study identifies an intrinsically disordered region in mouse ATE1, contrasting with yeast ATE1, and suggests its role in facilitating complex formation with tRNAArg.

This study compares AlphaFold2's pLDDT metric with NMR and computational dynamics metrics, finding that AlphaFold2 poorly captures the gradations of protein dynamics observed by NMR.

This paper uses simulations to show that sequence complexity and monomer rigidity determine the morphology and aging dynamics of protein aggregates.

CCfrag improves coiled-coil structural prediction by fragmenting sequences and using AlphaFold, enhancing accuracy and avoiding spurious models.

The paper investigates the role of the C-β4 loop in protein kinase structure and dynamics, showing its importance in hydrophobic spine architecture and communication between kinase lobes.

This study investigates how the WX conserved sequence motif modulates the conformation of the nSrc loop in SH3 domains, affecting ligand specificity.

The paper investigates the evolutionary dynamics of self-assembly in prokaryotic citrate synthases, finding frequent transitions between different assembly types without strong functional consequences.

This study models the full-length Epstein-Barr virus LMP1 protein and identifies potential drug targets in its C-terminus domain.