Protein Structure and Dynamics

Scop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein function

Scop3P-Toolkit provides an open-source framework for integrating PTMs, mutations, and proteomics data with structural and functional annotations to enable reproducible analysis.

Sequence adaptations satisfy the constraints of mitochondrial membrane protein evolution

The paper identifies aliphatic-to-threonine substitutions as a conserved adaptation in mitochondrial membrane proteins that balances hydrophilicity and hydrophobicity requirements.

FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications

FLIP2 adds seven protein fitness datasets and 16 splits for enzymes, light-sensitive proteins, and interactions; simple ridge and zero-shot baselines often rival fine-tuned protein language models.

De novo design of a protein fold for small-molecule binding through aromatic π stacking

This paper designs a de novo protein fold that binds doxorubicin with high affinity through aromatic π-stacking, revealing a new 5-helix globular fold.

Coevolution-informed Bayesian optimization for sample-efficient protein design

This paper introduces ALSEBO, a Bayesian optimization method for protein design that efficiently finds optimal sequences with few evaluations by leveraging coevolutionary statistics.

Incidental conformational switching in an allosteric enzyme

This study shows that yeast chorismate mutase exhibits incidental conformational switching, challenging the traditional two-state allosteric model by demonstrating decoupling between conformational state and catalytic activity.

Transient interdomain interactions shape the conformational ensemble governing RNA recognition by the tandem RRMs of Sex-lethal

This study shows that RNA recognition by the Sxl protein depends on a dynamic conformational ensemble rather than a single structure, and perturbing this balance impairs RNA binding.

Functional pocketomes and complete allosteric maps of five protein kinases

Energy-model maps of five human kinases show conserved distance-dependent decay of inhibitory allostery, but distal allosteric pockets and activating sites diverge between kinases.

Conformational diversity in poly-HAMP arrays and its implications for signal transduction

The paper investigates conformational diversity in poly-HAMP arrays and shows that axial helix rotation may be a conserved mechanism for signal transduction across different HAMP-containing systems.

HDOCK-Multimer: integrating docking and combinatorial assembly for structure prediction of large protein complexes

HDOCK-Multimer improves prediction of large protein complexes by combining docking and combinatorial assembly, outperforming existing methods on benchmark datasets.

Two activation heat capacity regimes underlie temperature-dependent catalysis in homologous archaeal ADP-dependent kinases

The paper investigates temperature-dependent catalysis in three homologous archaeal ADP-dependent kinases, identifying two distinct activation heat capacity regimes in two enzymes and a single regime in the third.

AdaptivePy: a unified Python framework for adaptive sampling in molecular dynamics

AdaptivePy provides a unified framework for adaptive sampling in MD simulations, implementing nine seed-selection policies and enabling meta adaptive sampling schemes.

Thermodynamic Profiling of Glucose Translocation in POPC embedded GLUT-4 protein models

This study compares the thermodynamic behavior of glucose translocation in GLUT4 using Cryo-EM and AlphaFold models, revealing structural limitations in AI-generated models.

Unified Sampling and Ranking for Protein Docking with DFMDock

DFMDock is a diffusion model for protein docking that combines generative sampling and energy-based ranking, achieving higher success rates than existing methods.

Investigating Enzyme Function by Geometric Matching of Catalytic Motifs

The paper develops a geometric matching method to detect catalytic features in protein structures, showing it is more sensitive than sequence-based approaches for identifying homology between distantly related enzymes.

Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization

This study uses molecular dynamics simulations to show that spacer heterogeneity in stickers-and-spacers polymers promotes condensation but reduces condensate organization and compositional robustness.

SpinForecast: chain-free probabilistic backbone assignment of intrinsically disordered proteins from NMR chemical shifts

SpinForecast assigns residue-specific chemical shifts to disordered proteins without sequential chain building, achieving high accuracy in peak assignment for three test proteins.

Structural basis for monobody OP-4 binding to open-form adenylate kinase

The paper determines the crystal structure of the OPEN-form adenylate kinase/monobody OP-4 complex and identifies key residues critical for binding.

HInt: interaction-based homology discovery through accelerated genome-scale AlphaFold screening

HInt uses AlphaFold to predict protein interactions and identifies homologous proteins by conserved interaction interfaces, revealing previously unknown relationships in prokaryotic and eukaryotic systems.

A Conserved Flexible N-Terminal Domain Tunes the Calcium Sensitivity of Sorcin by Stabilizing Its Active Conformation

This study identifies the flexible N-terminal domain of Sorcin as a critical regulator that enhances Ca2+ responsiveness by stabilizing its active conformation through dynamic contacts.

MAXWELL: Calibrating the probabilistic outputs of protein language models to the mutation-induced stability change landscape

MAXWELL calibrates protein language models to predict mutation-induced stability changes, outperforming existing methods and successfully designing stabilizing mutations in DhaA dehalogenase.

Kukulu: Diffusion-Based Reconstruction of Antibody CDR Loops using a Structure-Aware Joint Embedding Predictive Architecture

Kukulu reconstructs antibody CDR loops using a diffusion model with a structure-aware architecture, improving loop design by integrating sequence-structure constraints.

TriGraphQA: a triple graph learning framework for model quality assessment of protein complexes

TriGraphQA improves model quality assessment of protein complexes by using a triple graph framework that distinguishes intra-chain and inter-chain features, outperforming existing methods on benchmark datasets.

Transfer learning from computed stability data for nanobody melting-temperature prediction

The paper predicts nanobody melting temperatures using transfer learning with computed stability data, finding that free-energy perturbation labels and sequence diversity improve predictions.

Blending physics-based and inverse folding models to disentangle variant effects on stability and function

The paper blends physics-based and inverse folding models to separate variant effects on protein stability and function, revealing distinct signatures for gain-of-function and loss-of-function variants.

Encounter-state over-anchoring governs productive PETase binding on PET surfaces

This study identifies post-adsorption alignment as a key bottleneck in PETase surface recognition and proposes a design strategy to improve productive binding.

A hotspot for conformational heterogeneity driven by proline isomerisation in the androgen receptor disordered N-terminal domain

This study identifies a conserved proline-rich region in the androgen receptor N-terminal domain that shows conformational heterogeneity driven by cis proline conformers, modulated by phosphorylation and mutations.

HaloMPNN: retraining ProteinMPNN on halophilic proteomes for salt-tolerant enzyme design

This paper retrained ProteinMPNN on halophilic proteomes to design salt-tolerant enzymes, showing HaloMPNN shifts protein properties toward halophilic traits.

De novo design of small-molecule-induced conformational change

This paper designs de novo proteins that undergo small-molecule-induced conformational changes, demonstrating strong binding affinity and specificity for exatecan.

Seed-Guided De Novo Design Expands the Structural Diversity of Antitoxin Protein Binders

This paper introduces seed-guided diffusion-based design to improve structural diversity and target contact in antitoxin protein binders, achieving functional binders with enhanced selectivity.