Ryusei Ogino
@uudondondBeginner at computational chemistry / biomolecular MD simulations for drug discovery / amber, gromacs, openMM
🦠 We’re excited to announce our first competition in partnership with @asap_discovery and @openmsf! Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro: 🧩 Ligand Poses: Given a training set of SARS-CoV-2 Mpro X-ray structures, predict…
The #podcast is back! Episode 21 of Phase Space Invaders features Tamar Schlick as a guest, you can listen to it on Spotify or other platforms: open.spotify.com/episode/0TGl3p… In the spirit of interdisciplinary exploration, Tamar explains the connections between #mathematics and…
MD simulations were used to study the dynamics of myosin’s inactive conformation and the effect of ATP binding to myosin, showing how an ATP analog modifies the structure and dynamics of myosin in a sequestered state. ow.ly/Fy1F50UbSik
The results of the 16th Critical Assessment of Structure Prediction (#CASP16) have been announced, marking significant advancements in protein structure prediction. This biennial event brings together leading research groups worldwide to evaluate and enhance computational methods…
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction @naturemethods 1. SurfDock introduces a novel diffusion-based model for protein–ligand docking, utilizing surface-level features to enhance prediction accuracy,…
Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations #MolecularDynamics pubs.acs.org/doi/10.1021/ac… @serdar_durdagi #JCIM Vol64 Issue21 #PharamceuticalModeling
Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS G12D #MolecularDynamics pubs.acs.org/doi/10.1021/ac… @VithaniNeha @ABalaeff @OpenEyeSoftware #JCIM Vol64 Issue21 #compchem
Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension • Introducing PepHAR: a cutting-edge, hotspot-driven generative model for peptide design that leverages energy-based hotspot sampling and autoregressive fragment extension to create peptides targeting…
Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody–Protein Complexes • This study uses short molecular dynamics (MD) simulations to analyze 20 antibody–protein complexes, revealing critical features of interactions like…
A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics 1. This study introduces NeuralMD, a machine learning framework tailored for extended-timescale molecular dynamics (MD) simulations in protein-ligand binding, addressing the…
Structure and Energetics of PET-Hydrolyzing Enzyme Complexes: A Systematic Comparison from Molecular Dynamics Simulations #MolecularDynamics pubs.acs.org/doi/10.1021/ac… #JCIM Vol64 Issue21 #compchem
DockFormer: Efficient Multi-Modal Receptor-Ligand Interaction Prediction using Pair Transformer • Introducing DockFormer: a streamlined model that combines receptor flexibility with efficient prediction for receptor-ligand interactions, excelling in both structure and binding…
P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching • Introducing P2DFlow, a cutting-edge generative model designed to predict protein conformational ensembles, leveraging SE(3) flow matching and enhanced by innovative prior knowledge from ESMFold…
New manuscript led by @DediWang97 just published in JCTC @JCIM_JCTC Big idea: deep learning works well for well sampled data. For limited data, human intuition/laws of physics might be better bet. Here, as an illustration for weighted ensemble method, we use SPIB (state…
CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis #MolecularDynamics pubs.acs.org/doi/10.1021/ac… @bruciaf1 @je_eberhardt @manuco17 @Joe_r_loeffler @moonii1020 @diogo_stmart @ForliLab #JCIM Vol64 Issue21 #compchem
Graph Curvature Flow-Based Masked Attention pubs.acs.org/doi/10.1021/ac… #JCIM Vol64 Issue21 #MachineLearning #DeepLearning
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries #VirtualScreening pubs.acs.org/doi/10.1021/ac… #JCIM Vol64 Issue21 #MachineLearning #DeepLearning
#HighlightOfTheWeek Enhanced sampling methods to identify protein configurations that match experiments. #compchem pubs.acs.org/doi/10.1021/ac…
How can AI + Physics Accelerate Molecular Glue Discovery? Designing molecular glues requires prior knowledge of specific protein conformations that reveal binding pockets at protein-protein interfaces. These pockets are critical targets for small molecules that induce proximity…
ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring pubs.acs.org/doi/10.1021/ac… @atwi_rasha #JCIM Vol64 Issue21 #ApplicationNote
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