Search Results - python property documentation*

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics by Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

“…Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics…”
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Pickaxe: a Python library for the prediction of novel metabolic reactions by Shebek, Kevin M., Strutz, Jonathan, Broadbelt, Linda J., Tyo, Keith E. J.

“… for a user’s application due to lack of exhaustive reaction rules, restriction to pre-computed networks, and difficulty in using the software due to lack of documentation…”
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PyL3dMD: Python LAMMPS 3D molecular descriptors package by Panwar, Pawan, Yang, Quanpeng, Martini, Ashlie

“…–property-relationship models using machine learning. Here, we describe a suite of open-source Python-based post-processing routines, called PyL3dMD, for calculating 3D descriptors…”
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pyPept: a python library to generate atomistic 2D and 3D representations of peptides by Ochoa, Rodrigo, Brown, J. B., Fox, Thomas

“…We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the FASTA, HELM, or recently-developed BILN notations…”
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PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies by Cao, Dong-Sheng, Liang, Yi-Zeng, Yan, Jun, Tan, Gui-Shan, Xu, Qing-Song, Liu, Shao

“… Herein, we developed a comprehensive python package to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for drug discovery. PyDPI…”
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Mordred: a molecular descriptor calculator by Moriwaki, Hirotomo, Tian, Yu-Shi, Kawashita, Norihito, Takagi, Tatsuya

“… It is freely available via GitHub. Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms…”
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Properties and Styles of Software Technology Tutorials by Arya, Deeksha M., Guo, Jin L. C., Robillard, Martin P.

“… We studied the design of tutorials in the software documentation landscape for five popular programming languages: Java, C#…”
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A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank by Smelter, Andrey, Astra, Morgan, Moseley, Hunter N. B.

“…) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecule…”
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Metis: a python-based user interface to collect expert feedback for generative chemistry models by Menke, Janosch, Nahal, Yasmine, Bjerrum, Esben Jannik, Kabeshov, Mikhail, Kaski, Samuel, Engkvist, Ola

“… Metis is a Python-based open-source graphical user interface (GUI), designed to solve this and enable the collection of chemists…”
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An automated framework for NMR chemical shift calculations of small organic molecules by Yesiltepe, Yasemin, Nuñez, Jamie R., Colby, Sean M., Thomas, Dennis G., Borkum, Mark I., Reardon, Patrick N., Washton, Nancy M., Metz, Thomas O., Teeguarden, Justin G., Govind, Niranjan, Renslow, Ryan S.

“… ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties…”
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PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank by Kunnakkattu, Ibrahim Roshan, Choudhary, Preeti, Pravda, Lukas, Nadzirin, Nurul, Smart, Oliver S., Yuan, Qi, Anyango, Stephen, Nair, Sreenath, Varadi, Mihaly, Velankar, Sameer

“… PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions…”
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Digitalization of Legacy Datasets and Machine Learning Regression Yields Insights for Reservoir Property Prediction and Submarine-Fan Evolution: A Subsurface Example From the Lewis Shale, Wyoming by Martin, Thomas, Tadla, Jared, Jobe, Zane

“…Machine-learning algorithms have long aided in geologic property prediction from well-log data, but are primarily used to classify lithology, facies, formation, and rock types…”
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Simulation and Exergy Analysis of Energy Conversion Processes Using a Free and Open-Source Framework—Python-Based Object-Oriented Programming for Gas- and Steam Turbine Cycles by Zoder, Marius, Balke, Janosch, Hofmann, Mathias, Tsatsaronis, George

“… Relevant basics of a thermodynamic analysis with exergy-based methods and necessary fluid property models are explained…”
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TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson by Brammer, Jan C., Blanke, Gerd, Kellner, Claudia, Hoffmann, Alexander, Herres-Pawlis, Sonja, Schatzschneider, Ulrich

“… Use of the Python NetworkX graph library facilitated a compact and easily extensible implementation. Graphical Abstract…”
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GRANAD - Simulating GRAphene nanoflakes with ADatoms by Dams, David, Kosik, Miriam, Müller, Marvin, Ghosh, Abhishek, Babaze, Antton, Szczuczko, Julia, Bryant, Garnett W., Ayuela, Andrés, Rockstuhl, Carsten, Pelc, Marta, Słowik, Karolina

“…GRANAD is a program based on the tight-binding approximation to simulate optoelectronic properties of graphene nanoflakes and Su–Schrieffer–Heeger (SSH…”
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The NeuroML ecosystem for standardized multi-scale modeling in neuroscience by Sinha, Ankur, Gleeson, Padraig, Marin, Bóris, Dura-Bernal, Salvador, Panagiotou, Sotirios, Crook, Sharon, Cantarelli, Matteo, Cannon, Robert C, Davison, Andrew P, Gurnani, Harsha, Silver, Robin Angus

“…Data-driven models of neurons and circuits are important for understanding how the properties of membrane conductances, synapses, dendrites, and the anatomical connectivity between neurons generate…”
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GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations by Freitas Gustavo, Michael, Verstraelen, Toon

“…In this work we explore the properties which make many real-life global optimization problems extremely difficult to handle, and some of the common techniques used in literature to address…”
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PmagPy: Software package for paleomagnetic data analysis and a bridge to the Magnetics Information Consortium (MagIC) Database by Tauxe, L., Shaar, R., Jonestrask, L., Swanson‐Hysell, N. L., Minnett, R., Koppers, A. A. P., Constable, C. G., Jarboe, N., Gaastra, K., Fairchild, L.

“… The PmagPy software package is a cross‐platform and open‐source set of tools written in Python for the analysis of paleomagnetic data that serves as one interface to MagIC, accommodating various levels of user expertise…”
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ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database by Dong, Jie, Wang, Ning-Ning, Yao, Zhi-Jiang, Zhang, Lin, Cheng, Yan, Ouyang, Defang, Lu, Ai-Ping, Cao, Dong-Sheng

“…) properties and various toxicities (T). Therefore, rapid ADMET evaluation is urgently needed to minimize failures in the drug discovery process…”
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Role-Based Smart Contract: An Intelligent System for Scholarly Communication by Sivakumar, Eashwar, Chawla, Paras

“… All of these difficulties add to a lack of trust and degrade academics' reputations. These challenges can be addressed using blockchain because of its properties and its ability to do smart contracts…”
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