[HTML][HTML] Deep learning for genomics: from early neural nets to modern large language models

T Yue, Y Wang, L Zhang, C Gu, H Xue, W Wang… - International Journal of …, 2023 - mdpi.com
The data explosion driven by advancements in genomic research, such as high-throughput
sequencing techniques, is constantly challenging conventional methods used in genomics …

Deep learning for genomics: A concise overview

T Yue, Y Wang, L Zhang, C Gu, H Xue, W Wang… - arxiv preprint arxiv …, 2018 - arxiv.org
Advancements in genomic research such as high-throughput sequencing techniques have
driven modern genomic studies into" big data" disciplines. This data explosion is constantly …

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 …

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Y Yang, J Gao, J Wang, R Heffernan… - Briefings in …, 2018 - academic.oup.com
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

M Spencer, J Eickholt, J Cheng - IEEE/ACM transactions on …, 2014 - ieeexplore.ieee.org
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary
structure predictions, which are increasingly demanded due to the rapid discovery of …

MUFOLD‐SS: New deep inception‐inside‐inception networks for protein secondary structure prediction

C Fang, Y Shang, D Xu - Proteins: Structure, Function, and …, 2018 - Wiley Online Library
Protein secondary structure prediction can provide important information for protein 3D
structure prediction and protein functions. Deep learning offers a new opportunity to …

Classification of nuclear receptors based on amino acid composition and dipeptide composition

M Bhasin, GPS Raghava - Journal of Biological Chemistry, 2004 - jbc.org
Nuclear receptors are key transcription factors that regulate crucial gene networks
responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a …

Small-molecule ligand docking into comparative models with Rosetta

SA Combs, SL DeLuca, SH DeLuca, GH Lemmon… - Nature protocols, 2013 - nature.com
Abstract Structure-based drug design is frequently used to accelerate the development of
small-molecule therapeutics. Although substantial progress has been made in X-ray …

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

N Alam, O Goldstein, B **a, KA Porter… - PLoS computational …, 2017 - journals.plos.org
Peptide-protein interactions contribute a significant fraction of the protein-protein
interactome. Accurate modeling of these interactions is challenging due to the vast …

Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes

XB Zhou, C Chen, ZC Li, XY Zou - Journal of theoretical biology, 2007 - Elsevier
With the rapid increment of protein sequence data, it is indispensable to develop automated
and reliable predictive methods for protein function annotation. One approach for facilitating …