Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview

V Salmaso, S Moro - Frontiers in pharmacology, 2018 - frontiersin.org
Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

E Yuriev, J Holien, PA Ramsland - Journal of Molecular …, 2015 - Wiley Online Library
Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

Graphics processing units in bioinformatics, computational biology and systems biology

MS Nobile, P Cazzaniga, A Tangherloni… - Briefings in …, 2017 - academic.oup.com
Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …

DARC: mapping surface topography by ray-casting for effective virtual screening at protein interaction sites

R Gowthaman, SA Miller, S Rogers… - Journal of medicinal …, 2016 - ACS Publications
Protein–protein interactions represent an exciting and challenging target class for
therapeutic intervention using small molecules. Protein interaction sites are often devoid of …

DARC 2.0: improved docking and virtual screening at protein interaction sites

R Gowthaman, S Lyskov, J Karanicolas - PLOS one, 2015 - journals.plos.org
Over the past decade, protein-protein interactions have emerged as attractive but
challenging targets for therapeutic intervention using small molecules. Due to the relatively …

State-of-the-art GPGPU applications in bioinformatics

N Papangelopoulos, D Vlachakis, A Filntisi… - International Journal of …, 2013 - igi-global.com
The exponential growth of available biological data in recent years coupled with their
increasing complexity has made their analysis a computationally challenging process …

Computational screening and design for compounds that disrupt protein-protein interactions

DK Johnson, J Karanicolas - Current topics in medicinal …, 2017 - ingentaconnect.com
Protein-protein interactions play key roles in all biological processes, motivating numerous
campaigns to seek small-molecule disruptors of therapeutically relevant interactions. Two …

[PDF][PDF] Integración en Scipion del software de docking molecular Rosetta DARC para su aplicación en descubrimiento y reposicionamiento de fármacos

AM PARRA PÉREZ - i2pc.es
El cribado virtual basado en estructuras es una técnica in silico utilizada para filtrar grandes
bases de datos de compuestos en busca de moléculas que tenga una actividad deseada …

Characterizing a structural and functional model of nitric oxide reductase performing NO and O2 reduction in engineered myoglobin

JH Reed - 2017 - ideals.illinois.edu
Nitric oxide reductase (NOR) is a membrane-bound metalloenzyme in the denitrification
pathway of many bacteria. NORs are structurally homologous to subunit I of HCOs (heme …