Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

AS Rifaioglu, H Atas, MJ Martin… - Briefings in …, 2019 - academic.oup.com
The identification of interactions between drugs/compounds and their targets is crucial for
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …

[HTML][HTML] Artificial intelligence in pharmaceutical sciences

M Lu, J Yin, Q Zhu, G Lin, M Mou, F Liu, Z Pan, N You… - Engineering, 2023 - Elsevier
Drug discovery and development affects various aspects of human health and dramatically
impacts the pharmaceutical market. However, investments in a new drug often go …

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

S Mosalaganti, A Obarska-Kosinska, M Siggel… - Science, 2022 - science.org
INTRODUCTION The eukaryotic nucleus protects the genome and is enclosed by the two
membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear …

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

J Cubuk, JJ Alston, JJ Incicco, S Singh… - Nature …, 2021 - nature.com
Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein
critical for viral genome packaging, yet the molecular details that underlie this process are …

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

W Lee, M Tonelli, JL Markley - Bioinformatics, 2015 - academic.oup.com
SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for
NMR data analysis, despite the fact that development of the package by its originators …

Comparative protein structure modeling using MODELLER

B Webb, A Sali - Current protocols in bioinformatics, 2016 - Wiley Online Library
Comparative protein structure modeling predicts the three‐dimensional structure of a given
protein sequence (target) based primarily on its alignment to one or more proteins of known …

Protein structure prediction on the Web: a case study using the Phyre server

LA Kelley, MJE Sternberg - Nature protocols, 2009 - nature.com
Determining the structure and function of a novel protein is a cornerstone of many aspects of
modern biology. Over the past decades, a number of computational tools for structure …

Comparative protein structure modeling using Modeller

N Eswar, B Webb, MA Marti‐Renom… - Current protocols in …, 2006 - Wiley Online Library
Functional characterization of a protein sequence is one of the most frequent problems in
biology. This task is usually facilitated by accurate three‐dimensional (3‐D) structure of the …

NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning

MS Klausen, MC Jespersen, H Nielsen… - Proteins: Structure …, 2019 - Wiley Online Library
The ability to predict local structural features of a protein from the primary sequence is of
paramount importance for unraveling its function in absence of experimental structural …

Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death

C Silvestre-Roig, Q Braster, K Wichapong, EY Lee… - Nature, 2019 - nature.com
The perpetuation of inflammation is an important pathophysiological contributor to the global
medical burden. Chronic inflammation is promoted by non-programmed cell death,; …