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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…
Rapid developments of AI tools are expected to offer unprecedented assistance to the research of natural science including chemistry. However, neither existing unimodal task-specific specialist models nor emerging general large multimodal…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present…
Product Data Management (PDM) desktop and web based systems maintain the organizational technical and managerial data to increase the quality of products by improving the processes of development, business process flows, change management,…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
There is growing interest in graph pattern mining (GPM) problems such as motif counting. GPM systems have been developed to provide unified interfaces for programming algorithms for these problems and for running them on parallel systems.…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…
This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share…
The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due…
Computational Grids are emerging as a platform for next-generation parallel and distributed computing. Large-scale parametric studies and parameter sweep applications find a natural place in the Grid?s distribution model. There is little or…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types…
We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
We present QDK/Chemistry, a software toolkit for quantum chemistry workflows targeting quantum computers. The toolkit addresses a key challenge in the field: while quantum algorithms for chemistry have matured considerably, the…
In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…