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Dopants can tune the performance of MoS2 in various applications, but use of molecular dynamics simulations for doped MoS2 materials discovery is limited by the lack of multi-dopant interatomic potentials. Universal machine learning…
Scientific software is one of the key elements for reproducible research. However, classic publications and related scientific software are typically not (sufficiently) linked, and it lacks tools to jointly explore these artefacts. In this…
Merlin++ is a C++ charged-particle tracking library developed for the simulation and analysis of complex beam dynamics within high energy particle accelerators. Accurate simulation and analysis of particle dynamics is an essential part of…
Summary: HTSeq 2.0 provides a more extensive API including a new representation for sparse genomic data, enhancements in htseq-count to suit single cell omics, a new script for data using cell and molecular barcodes, improved documentation,…
We introduce Docling, an easy-to-use, self-contained, MIT-licensed, open-source toolkit for document conversion, that can parse several types of popular document formats into a unified, richly structured representation. It is powered by…
We present version 2.3 of SModelS, a public tool for the fast reinterpretation of LHC searches for new physics on the basis of simplified-model results. The main new features are a database update with the latest available experimental…
Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has…
Deep metric learning algorithms have a wide variety of applications, but implementing these algorithms can be tedious and time consuming. PyTorch Metric Learning is an open source library that aims to remove this barrier for both…
The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary…
Background: Data mining and analyzing of public Git software repositories is a growing research field. The tools used for studies that investigate a single project or a group of projects have been refined, but it is not clear whether the…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
OpenML is an online platform for open science collaboration in machine learning, used to share datasets and results of machine learning experiments. In this paper we introduce OpenML-Python, a client API for Python, opening up the OpenML…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
rigidPy is a Python package that provides a set of tools necessary for studying rigidity and mechanical response in spring networks. It also includes suitable modules for generating new realizations of networks with applications in glassy…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…
OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the…
Fitting models to measured data is one of the standard tasks in the natural sciences, typically addressed early on in physics education in the context of laboratory courses, in which statistical methods play a central role in analysing and…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…