Frontiers in Bioinformatics | Protein Bioinformatics

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

2,193 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

1,114 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

3,231 views
9 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

2,258 views
14 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

2,363 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

7,047 views
12 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

5,143 views
16 citations

Original Research

Published on 20 Jun 2023

Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode

in Protein Bioinformatics

Nour Nissan
Julia Hooker
Eric Arezza
Kevin Dick
Ashkan Golshani
Benjamin Mimee
Elroy Cober
James Green
Bahram Samanfar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1199675

2,349 views
2 citations

Editorial

Published on 22 May 2023

Editorial: Protein recognition and associated diseases

in Protein Bioinformatics

M. Michael Gromiha
Petras Kundrotas
Marcelo Adrian Marti
Česlovas Venclovas
Minghui Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1215141

1,285 views

Original Research

Published on 20 Apr 2023

Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events

in Protein Bioinformatics

Arnaud Kress
Olivier Poch
Odile Lecompte
Julie D. Thompson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1178926

2,436 views
7 citations

Original Research

Published on 06 Apr 2023

Orthogonal analysis of variants in APOE gene using in-silico approaches reveals novel disrupting variants

in Protein Bioinformatics

Chang Li
Ian Hou
Mingjia Ma
Grace Wang
Yongsheng Bai
Xiaoming Liu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1122559

2,610 views

Mini Review

Published on 28 Feb 2023

Before and after AlphaFold2: An overview of protein structure prediction

in Protein Bioinformatics

Letícia M. F. Bertoline
Angélica N. Lima
Jose E. Krieger
Samantha K. Teixeira

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1120370

67,782 views
152 citations

Original Research

Published on 17 Feb 2023

Virulence network of interacting domains of influenza a and mouse proteins

in Protein Bioinformatics

Teng Ann Ng
Shamima Rashid
Chee Keong Kwoh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1123993

2,040 views
1 citation

Original Research

Published on 16 Jan 2023

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution

in Protein Bioinformatics

Pierre Tufféry
Philippe Derreumaux

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1113928

2,860 views
6 citations

Original Research

Published on 06 Jan 2023

The META tool optimizes metagenomic analyses across sequencing platforms and classifiers

in Protein Bioinformatics

Robert A. Player
Angeline M. Aguinaldo
Brian B. Merritt
Lisa N. Maszkiewicz
Oluwaferanmi E. Adeyemo
Ellen R. Forsyth
Kathleen J. Verratti
Brant W. Chee
Sarah L. Grady
Christopher E. Bradburne

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.969247

3,909 views

Perspective

Published on 15 Dec 2022

On the choice of negative examples for prediction of host-pathogen protein interactions

in Protein Bioinformatics

Don Neumann
Soumyadip Roy
Fayyaz Ul Amir Afsar Minhas
Asa Ben-Hur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1083292

2,270 views
2 citations