Protein Structure and Dynamics

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments

Structome-AlignViewer evaluates structure-aware alignments by mapping alignment columns to protein structures and providing confidence scores to identify reliable regions.

Fold or flop: quality assessment of AlphaFold predictions on whole proteomes

The paper evaluates AlphaFold predictions using a new scoring function and identifies three structural populations in proteomes.

Exploring the GM-CSF Histidine Triad as a Modulator of Structure, Molecular Motion, and Ligand Binding

This study investigates how histidine residues in GM-CSF affect its structure, flexibility, and ligand binding at physiological pH.

Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness

This study uses simulations to show how varying stiffness in polymers affects their collapse and adsorption in crowded environments, with flexible regions promoting collapse and semiflexible regions influencing adsorption.

Computational redesign of a thermostable T7 RNA polymerase

This paper computationally redesigns T7 RNA polymerase to increase its thermal stability, achieving a T50 of 54.9°C with 59% wild-type activity at 37°C.

Simulation of Protein Structure using a Coarse-Grained Potential incorporating the Backbone Dihedral Interactions

The paper develops a coarse-grained protein model that retains backbone dihedral angles, reproducing structural details from crystal structures and all-atom simulations.

Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways

PRISM clusters molecular pathways using structural medoids and geometric dissimilarities, showing robust clustering across complex biomolecular transitions.

Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N

This study uses molecular dynamics simulations to analyze how CENP-N interacts with CENP-A nucleosomes, revealing structural changes and their impact on conformational states and protein interactions.

Accurate interdomain contacts in mixed folded proteins from NMR-guided coarse-grained simulations

The paper improves the accuracy of interdomain contacts in mixed folded-disordered proteins using NMR-guided coarse-grained simulations.

Evaluating transformer-based models for structural characterization of orphan proteins

The paper evaluates transformer-based models' ability to predict structural features of orphan proteins and finds they perform poorly on these sequences compared to homologous proteins.

Nearest Neighbour Interactions between Amino Acid Residues in Short Peptides and Coil Libraries

The paper compares conformational propensities of amino acid residues from GXYG peptides and XY dimers in a coil library, revealing discrepancies that suggest coil libraries may not fully capture statistical coil characteristics of IDPs and IDRs.

DeepPath: Overcoming data scarcity for protein transition pathway prediction using physics-based deep learning

DeepPath predicts protein transition pathways using physics-based deep learning, achieving accurate results faster than molecular dynamics simulations.

De novo design of metalloproteases for targeted amyloid-β cleavage

This paper designs metalloproteases that specifically cleave targeted peptide bonds in amyloid-β using a generative model, achieving high specificity and catalytic efficiency.

Disobind: a sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions

Disobind predicts inter-protein contact maps and interface residues for intrinsically disordered regions using sequence-based deep learning, outperforming existing methods without requiring structures or alignments.

Characterizing the fragmentation of AlphaFold predictions

The paper introduces new quantitative measures to assess AlphaFold predictions by analyzing pLDDT values along protein sequences.

Mapping Functional Dynamics Hotspots for Protein Engineering with NMR Peak Intensity Analysis

This study uses NMR peak intensity analysis to identify functional dynamics hotspots in proteins, showing that specific structural flexibility correlates with function in red fluorescent proteins.

Evolution tunes functional sub-state interconversion to boost enzyme function

This paper shows how evolution improves enzyme function by shifting the rate-limiting step from substrate binding to sub-state interconversion in β-lactamase OXA-48.

Correlated dynamics, reactive conformations and non-Arrhenius behaviour in the temperature-dependence of enzyme activity: triosephosphate isomerase

This study investigates the temperature dependence of triosephosphate isomerase activity using experiments and simulations, revealing non-Arrhenius behavior and dynamical differences between enzymes from different organisms.

Optimizing stability in dynamic small-molecule binding proteins

This study designs stabilized variants of dynamic periplasmic binding proteins by considering mutations compatible with both conformations, improving thermal stability without compromising ligand binding.

Probing the Structural Dynamics of the Unbound MAX Protein: Insights from Well-Tempered Metadynamics

This study uses well-tempered metadynamics to explore the conformational space of unbound MAX protein, revealing a stable structure and potential druggable sites for targeting MYC/MAX interactions.

To Predict is to Design: Unlocking Generative Capabilities in All-Atom Structure Predictors via Geometric Score Distillation

This paper introduces DREAM, a framework that enables protein design by inverting all-atom diffusion predictors, allowing gradient-based optimization of complex modalities like cyclic peptides.

Sampling Function-Related Metastable States of Proteins With DASH

DASH samples function-related metastable states of proteins, revealing new folding states and allosteric sites, verified by experiments and crystal structures.

Intrinsic Error Correction in Protein Allostery: Quantifying Noise Suppression via Spanning Tree Statistics

The paper quantifies noise suppression in protein allostery by analyzing communication pathways and their topology-aware weighting across multiple proteins.

Clearing the whey: Efficient inhibition and removal of chymosin from whey by de novo designed protein-based inhibitors

The paper designs protein-based inhibitors to efficiently inhibit and remove chymosin from whey, enabling sustainable cheese production and enzyme control.

Evidence for the Progressive Improvement of All-Atom Force Fields in Reproducing Local Conformational Preferences of Flexible Peptides

The paper evaluates improvements in all-atom force fields for modeling flexible peptides by comparing conformational ensembles to experimental data.

How Much Does Protein Structure Really Help? A Case Study in Mutation-Induced Stability Prediction

This paper investigates whether protein structure improves mutation-induced stability prediction, finding that sequence embeddings dominate and structure provides limited additive value in most cases.

Implicit modeling of the conformational landscape and sequence allows scoring and generation of stable proteins

This study presents a joint optimization approach for modeling protein conformational landscapes and sequence design, showing improved stability prediction and sequence generation.

MONDE·T: A Database and Interactive Webserver for Non-Canonical Amino Acids (ncAAs) in the PDB

The paper introduces MONDE·T, a database and webserver for non-canonical amino acids in the PDB, providing structural analysis and visualization tools.

Molecular interactions underlying selective partitioning of clients into MED1 and FUS condensates

The paper uses simulations to study how proteins partition into MED1 and FUS condensates, identifying sequence features that predict partitioning and developing a sequence-based predictor.

Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM

This paper provides a tutorial on using ShapeGMM to cluster and sample biomolecular conformations from molecular dynamics simulations.