10 papers · ranked by Valyu relevance
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…
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…
Robert Shaw, Grant Hill
The basis set used in quantum chemical calculations for molecular applications is vital to the accuracy and efficiency of the calculation, but the development of novel basis sets is hindered by an opaque process and inaccessibility of the tools required. We present here BasisOpt, a tool for the automated optimization…
Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche + 3 more
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry…
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…
Antoine Lacour, Hamza Ibrahim, Andrea Volkamer, Anna K. H. Hirsch
In this study, we introduce DockM8, an innovative open-source platform designed for consensus virtual screening in drug design. Leveraging various docking algorithms and scoring functions, DockM8 provides a highly customizable workflow for structure-based virtual screening. In rigorous evaluations across the DEKOIS…
Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg + 4 more
Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement…
Rafael Temirgaliev, Dmitry Pavlov
We study methods of non-linear global optimization in the problem of molecular docking and present a new implementation of protein-ligand docking and preparation of molecules for docking in a new open source software Hess. It uses BFGS for local optimization and two different forms of Monte Carlo method for global…
Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg + 4 more
Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement…
Rıza Özçelik, Laura van Weesep, Sarah de Ruiter, Francesca Grisoni
In this work, we introduce peptidy -- a lightweight Python library that facilitates converting peptides (expressed as aminoacid sequences) to numerical representations suited to machine learning. peptidy is free from external dependencies, integrates seamlessly into modern Python environments, and supports a range of…