相关论文: MIMTool: A Tool for Drawing Molecular Interaction …
Learned world models hold significant potential for robotic manipulation, as they can serve as simulator for real-world interactions. While extensive progress has been made in 2D video-based world models, these approaches often lack…
Is it feasible to create an analysis paradigm that can analyze and then accurately and quickly predict known drugs from experimental data? PharML.Bind is a machine learning toolkit which is able to accomplish this feat. Utilizing deep…
Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the…
Mixed-integer programming (MIP) is a well-established framework for computer-aided molecular design (CAMD). By precisely encoding the molecular space and score functions, e.g., a graph neural network, the molecular design problem is…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
In vision-language pre-training (VLP), masked image modeling (MIM) has recently been introduced for fine-grained cross-modal alignment. However, in most existing methods, the reconstruction targets for MIM lack high-level semantics, and…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
TIM (The Interactive METATOY) is a ray-tracing program specifically tailored towards our research in METATOYs, which are optical components that appear to be able to create wave-optically forbidden light-ray fields. For this reason, TIM…
We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used…
Analyzing CT scans, MRIs and X-rays is pivotal in diagnosing and treating diseases. However, detecting and identifying abnormalities from such medical images is a time-intensive process that requires expert analysis and is prone to…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
Real-time semantic segmentation of LiDAR data is crucial for autonomously driving vehicles, which are usually equipped with an embedded platform and have limited computational resources. Approaches that operate directly on the point cloud…
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…
Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we…
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…
PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…
We present iSLAT (the Interactive Spectral-Line Analysis Tool), a python-based graphical tool that allows users to interactively explore and manually fit line emission observed in molecular spectra. iSLAT adopts a simple slab model that…