AI in drug discovery and its clinical relevance

R Qureshi, M Irfan, TM Gondal, S Khan, J Wu, MU Hadi… - Heliyon, 2023 - cell.com
The COVID-19 pandemic has emphasized the need for novel drug discovery process.
However, the journey from conceptualizing a drug to its eventual implementation in clinical …

Why are there hotspot mutations in the TP53 gene in human cancers?

EH Baugh, H Ke, AJ Levine, RA Bonneau… - Cell Death & …, 2018 - nature.com
The p53 gene contains homozygous mutations in~ 50–60% of human cancers. About 90%
of these mutations encode missense mutant proteins that span~ 190 different codons …

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

W Zheng, C Zhang, Y Li, R Pearce, EW Bell… - Cell reports methods, 2021 - cell.com
Structure prediction for proteins lacking homologous templates in the Protein Data Bank
(PDB) remains a significant unsolved problem. We developed a protocol, CI-TASSER, to …

Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology

M Bertoni, F Kiefer, M Biasini, L Bordoli, T Schwede - Scientific reports, 2017 - nature.com
Cellular processes often depend on interactions between proteins and the formation of
macromolecular complexes. The impairment of such interactions can lead to deregulation of …

Accurate de novo prediction of protein contact map by ultra-deep learning model

S Wang, S Sun, Z Li, R Zhang, J Xu - PLoS computational biology, 2017 - journals.plos.org
Motivation Protein contacts contain key information for the understanding of protein structure
and function and thus, contact prediction from sequence is an important problem. Recently …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

I-TASSER server: new development for protein structure and function predictions

J Yang, Y Zhang - Nucleic acids research, 2015 - academic.oup.com
The I-TASSER server (http://zhanglab. ccmb. med. umich. edu/I-TASSER) is an online
resource for automated protein structure prediction and structure-based function annotation …

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier

M Kulmanov, MA Khan, R Hoehndorf - Bioinformatics, 2018 - academic.oup.com
Motivation A large number of protein sequences are becoming available through the
application of novel high-throughput sequencing technologies. Experimental functional …

Protein secondary structure prediction using deep convolutional neural fields

S Wang, J Peng, J Ma, J Xu - Scientific reports, 2016 - nature.com
Protein secondary structure (SS) prediction is important for studying protein structure and
function. When only the sequence (profile) information is used as input feature, currently the …

Protein structure and function prediction using I‐TASSER

J Yang, Y Zhang - Current protocols in bioinformatics, 2015 - Wiley Online Library
I‐TASSER is a hierarchical protocol for automated protein structure prediction and structure‐
based function annotation. Starting from the amino acid sequence of target proteins, I …