Related papers: ProTDyn: a foundation Protein language model for T…
Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…
This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Protein design has become a critical method in advancing significant potential for various applications such as drug development and enzyme engineering. However, protein design methods utilizing large language models with solely pretraining…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by the computational cost. To address this, a surge of deep…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
Molecular dynamics (MD) is a central computational tool in physics, chemistry, and biology, enabling quantitative prediction of experimental observables as expectations over high-dimensional molecular distributions such as Boltzmann…