Related papers: Development & Implementation of a PyMOL 'putty' Re…
Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…
We embed several copies of the derived category of a quiver and certain line bundles in the derived category of an associated moduli space of representations, giving the start of a semiorthogonal decomposition. This mirrors the…
Programming for distributed memory machines has always been a tedious task, but necessary because compilers have not been sufficiently able to optimize for such machines themselves. Molly is an extension to the LLVM compiler toolchain that…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
An analytical function is derived that exactly describes the amplification process due to a series of discrete, Poisson-like amplifications like those in a photo multiplier tube (PMT). A numerical recipe is provided that implements this…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each $k$-point in the Brillouin zone and band in an electronic structure calculation.…
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models…
Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated…
Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
Automatic group emotion recognition plays an important role in understanding complex human-human interaction. This paper introduces, Emolysis, a Python-based, standalone open-source group emotion analysis toolkit for use in different social…
The Python colorspace package provides a toolbox for mapping between different color spaces which can then be used to generate a wide range of perceptually-based color palettes for qualitative or quantitative (sequential or diverging)…
Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for…
Interpreting samples from likelihood or posterior probability density functions is rarely as straightforward as it seems it should be. Producing publication-quality graphics of these distributions is often similarly painful. In this short…
Studying facial expressions is a notoriously difficult endeavor. Recent advances in the field of affective computing have yielded impressive progress in automatically detecting facial expressions from pictures and videos. However, much of…
In this study we have presented a novel feature representation for malicious programs that can be used for malware classification. We have shown how to construct the features in a bottom-up approach, and analyzed the overlap of malicious…
PySymmPol is a Python package designed for efficient manipulation of symmetric polynomials. It provides functionalities for working with various types of symmetric polynomials, including elementary, homogeneous, monomial symmetric, (skew-)…