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Found 7 papers, 4 papers with code
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico.
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years.
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena.
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
In this work, we present DiffPack, a torsional diffusion model that learns the joint distribution of side-chain torsional angles, the only degrees of freedom in side-chain packing, by diffusing and denoising on the torsional space.
Protein Sequence and Structure Co-Design with Equivariant Translation
Proteins are macromolecules that perform essential functions in all living organisms.
E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking
In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery.
ParaFold: Paralleling AlphaFold for Large-Scale Predictions
We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19, 704 small proteins in five hours on one NVIDIA DGX-2.
