9 papers · ranked by Valyu relevance
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…
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…
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…
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…
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…
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…