20 papers · ranked by Valyu relevance
Nir Goren, Efi Fogel, Dan Halperin
We introduce Python bindings that enable the convenient, efficient, and reliable use of software modules of Cgal (The Computational Geometry Algorithms Library), which are written in C++, from within code written in Python. There are different tools that facilitate the creation of such bindings. We present a short…
Yangyang Li, Rendong Yang
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows.…
Isabella Basso Amaral, Renato Cordeiro Ferreira, Alfredo Goldman
—The Python programming language is best known for its syntax and scientific libraries, but it is also notorious for its slow interpreter. Optimizing critical sections in Python entails special knowledge of the binary interactions between program ming languages, and can be cumbersome to interface manually, with…
Yangyang Li, Rendong Yang
Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern…
Martin Larralde, Georg Zeller, Can Alkan
Protein similarity search and annotation is a key part of biological sequence analysis, allowing for the discovery of protein function from sequence data. Improving on Position-Specific Scoring Matrices that were used historically to search for motifs, Profile Hidden Markov Models (pHMMs) were introduced in HMMER () to…
Patrick Stowell, Robert Foster, Almahdi Elhamri
GEANT4 is a particle physics simulation tool used to develop and optimize radiation detectors. While C++-based examples exist, Python's growing popularity necessitates the development of a more accessible Python bindings interface. This work demonstrates the use of cppyy, the automated C++-Python binding package, to…
M. Eric Irrgang, Caroline Davis, Peter M. Kasson, Dina Schneidman-Duhovny
'Dina Schneidman-Duhovny'] Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line…
Wanling Song, Robin A. Corey, T. Bertie Ansell, C. Keith Cassidy + 4 more
Interactions from Molecular Dynamics Simulations Authors: ['Wanling Song' 'Robin A. Corey' 'T. Bertie Ansell' 'C. Keith Cassidy' 'Michael R. Horrell' 'Anna L. Duncan' 'Phillip J. Stansfeld' 'Mark S. P. Sansom'] Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations…
Hao Li, Gopi Krishnan Rajbahadur, Cor‐Paul Bezemer
Learning Software Quality Authors: ['Hao Li' 'Gopi Krishnan Rajbahadur' 'Cor‐Paul Bezemer'] Bindings for machine learning frameworks (such as TensorFlow and PyTorch) allow developers to integrate a framework's functionality using a programming language different from the framework's default language (usually Python).…
Magnar Bjørgve, Christian Tantardini, Stig Rune Jensen, Gabriel A. Gerez S. + 4 more
Multiwavelets Representation Authors: ['Magnar Bjørgve' 'Christian Tantardini' 'Stig Rune Jensen' 'Gabriel A. Gerez S.' 'Peter Wind' 'Roberto Di Remigio' 'Evgueni Dinvay' 'Luca Frediani'] Wavelets and Multiwavelets have lately been adopted in Quantum Chemistry to overcome challenges presented by the two main families…
Tianyang Wang, Ziqian Bi, Keyu Chen, Jiawei Xu + 11 more
Management: Object-Oriented Programming Authors: ['Tianyang Wang' 'Ziqian Bi' 'Keyu Chen' 'Jiawei Xu' 'Qian Niu' 'Junyu Liu' 'Benji Peng' 'Ming Li' 'Sen Zhang' 'Xiaoyong Pan' 'Jinlang Wang' 'Pohsun Feng' 'Caitlyn Heqi Yin' 'Yizhu Wen' 'Ming Liu'] | III | Advancing Your Skills | | 9 | | --- | --- | --- | --- | | 1 |…
Erick Martins Ratamero, Kiya Govek, Julio Mateos Langerak, Fernando Cervantes Sanchez + 1 more
Many research laboratories need to manage, process, and analyze the increasingly large volumes and complexity of data being produced by state-of-the-art bioimaging platforms. OMERO is a popular open-source client-server application that provides a unified interface for managing and working with bioimages and their…
João Victor da Silva Guerra, Helder Veras Ribeiro-Filho, Gabriel Ernesto Jara, Leandro Oliveira Bortot + 2 more
Background Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and…
Keyu Xu, Zeyuan Di, Jianquan Zhao, Haicang Zhang + 1 more
Proteins are essential biological macromolecules that play a crucial role in living organisms. Protein-protein interactions, which govern various biological processes such as signal transduction, cell metabolism, and cell growth, are key aspect of protein function. The strength of these interactions, characterized by…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Leopold Endres, Tobias Olenyi, Kyra Erckert, Konstantin Weißenow + 2 more
Identifying residues in a protein involved in ligand binding is important for understanding its function. bindEmbed21DL is a Machine Learning method which predicts protein-ligand binding on a per-residue level using embeddings derived from the protein Language Model (pLM) ProtT5. This method relies solely on sequences…
Dimitar Georgiev, Simon Vilms Pedersen, Ruoxiao Xie, Álvaro Fernández-Galiana + 2 more
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Andrew McNutt, David Koes
Determination of the bound pose of a ligand is a critical first step in many in silico drug discovery tasks. Molecular docking is the main tool for the prediction of non-covalent binding of a protein and ligand system. Molecular docking pipelines often only utilize the information of one ligand binding to the protein…