12 papers · ranked by Valyu relevance
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…
Muhammad Aziz
Computational chemistry software designed to compute the chemical properties of compounds falls under the category of dry research. The computational calculation of chemicals is a broad term. In this current study, chemical properties are estimated through computational methods, which is valuable for newly synthesis…
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…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…
Martin Seifrid, Felix Strieth-Kalthoff, Mohammad Haddadnia, Tony Wu + 7 more
We introduce Chemspyd, a lightweight, open-source Python package for operating the popular laboratory robotic platforms from Chemspeed Technologies. As an add-on to the existing proprietary software suite, Chemspyd enables dynamic communication with the automated platform, laying the foundation for its modular…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…
Anselm W. Hahn, Joseph Zsombor-Pindera, Pierre Kennepohl, Serena DeBeer
In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows…
Kirill Zinovjev, Marc W. van der Kamp
Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained…
Kirill Zinovjev, Marc W. van der Kamp
X-ray crystallography allows detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. However, crystal structures provide little more than a static picture of proteinligand interactions, whereas dynamical…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…