Protein Structure and Dynamics

SHINE improves pathway ensemble analysis by integrating n-ary similarity, cheminformatics tools, and hierarchical clustering for MD simulations.

DIRseq predicts drug-interacting residues in intrinsically disordered proteins from sequences, showing good agreement with experimental methods like NMR and MD simulations.

This paper introduces a pre-training framework that combines sequential and geometric encoders to improve protein variant prediction for enhanced bioactivity and thermostability.

The paper benchmarks PSCP methods on CASP datasets, showing they work well with experimental data but struggle with AlphaFold-generated structures, and explores confidence-aware integration with limited success.

EVOLVE is a web platform that analyzes multi-sequence data to identify concerning variants using phase transition principles and provides tools for exploring mutational metrics.

This paper introduces CyclicChamp, a computational pipeline for designing cyclic peptides of 7-24 residues, achieving stable designs validated by molecular dynamics simulations.

This paper introduces an enhanced G[o]Martini model that improves protein dynamics simulation and addresses inaccuracies in the Martini protein model through diverse case studies.

This paper introduces wall-EASAL, a discrete geometry method for integrative protein docking using crosslinks, showing improved performance and efficiency over IMP.

PSTP predicts protein phase separation regions using transfer learning and attention, achieving 84% accuracy on PhaSePro and improving correlation coefficients over existing models.

This study uses molecular dynamics simulations and Markov state models to analyze histone tail conformations and shows acetylation increases H2B tail dynamics.

This study uses molecular dynamics simulations to identify active and inactive states of neurotrophin receptor transmembrane domains and suggests distinct signaling mechanisms for different receptors.

ChiraKit is an online tool that processes and analyzes circular dichroism data to calculate secondary structure, estimate helicity, fit unfolding models, and decompose spectra.

LoRA-DR-suite predicts intrinsic and soft disorder in proteins using adapter-based embeddings, with SoftDis providing a database of 500,000 PDB chains.

This paper introduces GSnet, a graph neural network for predicting protein molecular properties, and shows it outperforms existing methods for solvent-accessible surface area prediction.

The paper describes a method to identify cross-β forming regions in low complexity domains that mediate self-association and phase separation.

This study uses molecular dynamics simulations to analyze how DNA sequences affect the structural stability and binding affinity of the ZTA transcription factor and DNA complex, identifying ZRE 3 as the most stable and affinity-rich sequence.

The paper uses AlphaFold2 to predict protein interactions among nuage and piRNA-related proteins, validating several novel interactions through experimental methods.

NCPepFold predicts structures of non-canonical cyclic peptides with improved accuracy using multigranular representation and cyclization optimization.

The paper investigates how hereditary spastic paraplegia mutations affect katanin's conformational transition using molecular simulations, revealing that some mutations impact an intermediate state.

HighFold2 predicts 3D structures of cyclic peptides with unnatural amino acids, achieving a median RMSD of 1.891 Å for monomers and complexes.

This study investigates how NAD+, ATP, and oxidants induce conformational changes in GAPDH, revealing structural instability and subunit splitting under specific conditions.

mdciao provides an open-source tool for analyzing and visualizing molecular dynamics simulation data with automated figure generation and customizable analysis options.

This paper determines the structure of the palladin-actin complex using crosslinking, docking, NMR, and SAXS, revealing how palladin stabilizes F-actin at the interface between two actin monomers.

The paper shows that weak specific protein interactions in cellular compartments determine barnase stability, differing from in vitro and artificial crowding conditions.

This paper presents the structure and thermodynamic analysis of the extended RNA recognition motif in hnRNPR-like proteins, revealing a conserved tryptophan cage motif critical for folding and stability.

This study identifies that left-handed glycyl conformations protect against protein aggregation and enhance stability by disrupting beta-strand pairing.

This study investigates how environmental factors like pH and ionic strength affect the conformational and amyloidogenic properties of DPF3a using biophysical and molecular dynamics methods.

This study shows IP6 binding influences the kinetic switch of the HIV-1 capsid's TVGG motif between coil and helix conformations, essential for pentamer formation.

This study quantifies charge-based transient interactions in intrinsically disordered proteins, showing they shape conformational behavior and are enriched in specific biological functions.