Related papers: Multimodal Protein Language Models for Enzyme Kine…

We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…

Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…

The slow microstructural evolution of materials often plays a key role in determining material properties. When the unit steps of the evolution process are slow, direct simulation approaches such as molecular dynamics become prohibitive and…

Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…

Protein design aims to compose amino-acid sequences that fold into stable three-dimensional structures while satisfying targeted functional properties. The field is increasingly shifting toward vibe protein design, where a single model is…

Expressing universal semantics common to all languages is helpful in understanding the meanings of complex and culture-specific sentences. The research theme underlying this scenario focuses on learning universal representations across…

Accurate prediction of RNA-associated interactions is essential for understanding cellular regulation and advancing drug discovery. While Biological Large Language Models (BioLLMs) such as ESM-2 and RiNALMo provide powerful sequence…

Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…

Adapting pre-trained language models (PLMs) for time-series text classification amidst evolving domain shifts (EDS) is critical for maintaining accuracy in applications like stance detection. This study benchmarks the effectiveness of…

Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA…

Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…

Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a…

The high computational cost of evaluating atomic interactions recently motivated the development of computationally inexpensive kinetic models, which can be parametrized from MD simulations of complex chemistry of thousands of species or…

Predicting multiple functions labeled with Enzyme Commission (EC) numbers from the enzyme sequence is of great significance but remains a challenge due to its sparse multi-label classification nature, i.e., each enzyme is typically…

In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…

Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia coli is integral for detecting chemicals over a wide range of background concentrations, ultimately allowing cells to swim towards sources of attractant and away from…

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…

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…

Searching through chemical space is an exceptionally challenging problem because the number of possible molecules grows combinatorially with the number of atoms. Large, autoregressive models trained on databases of chemical compounds have…

A mathematical model to describe the emulsion polymerization kinetics of co- and ter-polymerizations is developed. The model is based on the classical Smith-Ewart (SE) equations, within the pseudo-homopolymerization approach, with…