Original Research

Published on 18 Oct 2024

DCMA: faster protein backbone dihedral angle prediction using a dilated convolutional attention-based neural network

in Protein Bioinformatics

Buzhong Zhang
Meili Zheng
Yuzhou Zhang
Lijun Quan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1477909

266 views

Review

Published on 04 Sep 2024

PhIP-Seq: methods, applications and challenges

in Protein Bioinformatics

Ziru Huang
Samarappuli Mudiyanselage Savini Gunarathne
Wenwen Liu
Yuwei Zhou
Yuqing Jiang
Shiqi Li
Jian Huang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1424202

2,105 views

Original Research

Published on 25 Jul 2024

A hybrid approach for predicting transcription factors

in Protein Bioinformatics

Sumeet Patiyal
Palak Tiwari
Mohit Ghai
Aman Dhapola
Anjali Dhall
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1425419

1,010 views

Perspective

Published on 20 Jun 2024

Bioinformatics proficiency among African students

in Protein Bioinformatics

Ashraf Akintayo Akintola
Abdullahi Tunde Aborode
Muhammed Taofiq Hamza
Augustine Amakiri
Benjamin Moore
Suliat Abdulai
Oluyinka Ajibola Iyiola
Lateef Adegboyega Sulaimon
Effiong Effiong
Adedeji Ogunyemi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1328714

1,864 views

Original Research

Published on 24 May 2024

Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

in Protein Bioinformatics

Phillip J. Tomezsko
Colby T. Ford
Avery E. Meyer
Adam M. Michaleas
Rafael Jaimes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1397968

1,711 views
6 citations

Original Research

Published on 23 Feb 2024

Computational identification of antibody-binding epitopes from mimotope datasets

in Protein Bioinformatics

Rang Li
Sabrina Wilderotter
Madison Stoddard
Debra Van Egeren
Arijit Chakravarty
Diane Joseph-McCarthy

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1295972

2,284 views

Technology and Code

Published on 09 Feb 2024

MARTin—an open-source platform for microarray analysis

in Protein Bioinformatics

Kai O. Kreissner
Benjamin Faller
Ivan Talucci
Hans M. Maric

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1329062

1,834 views
1 citation

Methods

Published on 31 Jan 2024

Making bioinformatics training FAIR: the EMBL-EBI training portal

in Protein Bioinformatics

A. L. Swan
A. Broadbent
P. Singh Gaur
A. Mishra
K. Gurwitz
A. Mithani
S. L. Morgan
G. Malhotra
C. Brooksbank

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1347168

1,608 views

Methods

Published on 26 Jan 2024

AlignScape, displaying sequence similarity using self-organizing maps

in Protein Bioinformatics

Isaac Filella-Merce
Vincent Mallet
Eric Durand
Michael Nilges
Guillaume Bouvier
Riccardo Pellarin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1321508

2,226 views

Original Research

Published on 05 Jan 2024

Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches

in Protein Bioinformatics

Patricia Soto
Davis T. Thalhuber
Frank Luceri
Jamie Janos
Mason R. Borgman
Noah M. Greenwood
Sofia Acosta
Hunter Stoffel

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1321287

1,420 views

Editorial

Published on 05 Jan 2024

Editorial: Expert opinions in protein bioinformatics: 2022

in Protein Bioinformatics

Daisuke Kihara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1338560

730 views

Original Research

Published on 18 Dec 2023

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

in Protein Bioinformatics

Kyohei Koyama
Kosuke Hashimoto
Chioko Nagao
Kenji Mizuguchi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1274599

2,127 views
5 citations

Methods

Published on 13 Dec 2023

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs

in Protein Bioinformatics

Paul Klemm
Peter F. Stadler
Marcus Lechner

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1322477

1,475 views
4 citations

Methods

Published on 17 Oct 2023

Protein quality assessment with a loss function designed for high-quality decoys

in Protein Bioinformatics

Soumyadip Roy
Asa Ben-Hur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1198218

1,691 views
1 citation

Original Research

Published on 17 Aug 2023

Improved prediction of MHC-peptide binding using protein language models

in Protein Bioinformatics

Nasser Hashemi
Boran Hao
Mikhail Ignatov
Ioannis Ch. Paschalidis
Pirooz Vakili
Sandor Vajda
Dima Kozakov

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1207380

5,308 views
10 citations

Perspective

Published on 27 Jul 2023

Current successes and remaining challenges in protein function prediction

in Protein Bioinformatics

Constance J. Jeffery

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1222182

3,655 views
8 citations

Navigation group

Articles

DCMA: faster protein backbone dihedral angle prediction using a dilated convolutional attention-based neural network

PhIP-Seq: methods, applications and challenges

A hybrid approach for predicting transcription factors

Bioinformatics proficiency among African students

Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

Computational identification of antibody-binding epitopes from mimotope datasets

MARTin—an open-source platform for microarray analysis

Making bioinformatics training FAIR: the EMBL-EBI training portal

AlignScape, displaying sequence similarity using self-organizing maps

Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches

Editorial: Expert opinions in protein bioinformatics: 2022

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs

Protein quality assessment with a loss function designed for high-quality decoys

Improved prediction of MHC-peptide binding using protein language models

Current successes and remaining challenges in protein function prediction