Frontiers in Bioinformatics | Protein Bioinformatics

Original Research

Published on 20 Oct 2025

Fish isoallergens and variants: database compilation, in silico allergenicity prediction challenges, and epitope-based threshold optimization

in Protein Bioinformatics

Vachiranee Limviphuvadh
Thimo Ruethers
Minh N. Nguyen
Dean R. Jerry
Benjamin P. C. Smith
Yulan Wang
Yansong Miao
Anand Kumar Andiappan
Andreas L. Lopata
Sebastian Maurer-Stroh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1669237

788 views

Original Research

Accepted on 14 Oct 2025

Uncovering human kinase substrates in the Nipah proteome

in Protein Bioinformatics

Vineetha Shaji
Akash Anil
Ayisha A Jabbar
Althaf Mahin
Ahmad Rafi
Sowmya Soman
Amjesh Revikumar
Dr.Ganesh Prasad
Dr. Sneha M. Pinto
Yashwanth Subbannayya

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1678189

226 views

Original Research

Accepted on 14 Oct 2025

Role of Histone-lysine N-methyltransferase 2D (KMT2D) in MEK-ERK signaling-mediated epigenetic regulation: A Phosphoproteomics perspective

in Protein Bioinformatics

Sreeshma Ravindran Kammarambath
Leona D’cunha
Athira Perunelly Gopalakrishnan
Amal Fahma
Neelam Krishna
Althaf Mahin
Samseera Ummar
Prathik Basthikoppa Shivamurthy
Inamul Hasan Madar
Rajesh Raju

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1683469

118 views

Original Research

Accepted on 07 Oct 2025

ParaDeep: Sequence-Based Deep Learning for Residue-Level Paratope Prediction Using Chain-Aware BiLSTM-CNN Models

in Protein Bioinformatics

Piyachat Udomwong
Thanathat Pamonsupornwichit
Kanchanok Kodchakorn
Chatchai Tayapiwatana

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1684042

243 views

Original Research

Accepted on 22 Sep 2025

Unravelling the Molecular Basis for snake venom NGF - human TrkA recognition through Molecular Dynamics Simulation and comparison with Human NGF

in Protein Bioinformatics

Shrudhi Devi
Jayaraman Gurunathan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1674791

292 views

Technology and Code

Published on 04 Sep 2025

Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

in Protein Bioinformatics

Grigorios Koulouras
Yingrong Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1576317

1,872 views

Original Research

Published on 01 Sep 2025

COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices

in Protein Bioinformatics

Rafael Pereira Lemos
Diego Mariano
Sabrina De Azevedo Silveira
Raquel C. de Melo-Minardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630078

924 views

Original Research

Published on 18 Jul 2025

IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions

in Protein Bioinformatics

Clara Shionyu-Mitusyama
Satoshi Ohmori
Subaru Hirata
Hirokazu Ishida
Tsuyoshi Shirai

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1627836

1,965 views

Original Research

Published on 17 Jul 2025

Understanding the selectivity in silico of colistin and daptomycin toward gram-negative and gram-positive bacteria, respectively, from the interaction with membrane phospholipids

in Protein Bioinformatics

Yesid Aristizabal
Yamil Liscano
José Oñate-Garzón

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1569480

1,441 views

Original Research

Published on 16 Jul 2025

Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation

in Protein Bioinformatics

Chelsy Chesterman
Thomas Desautels
Luz-Jeannette Sierra
Kathryn T. Arrildt
Adam Zemla
Edmond Y. Lau
Shivshankar Sundaram
Jason Laliberte
Lynn Chen
Aaron Ruby

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1580967

2,003 views

Original Research

Published on 25 Jun 2025

In-silico molecular analysis and blocking of the viral G protein of Nipah virus interacting with ephrin B2 and B3 receptor by using peptide mass fingerprinting

in Protein Bioinformatics

Ayesha Sajjad
Ihteshamul Haq
Rabia Syed
Faheem Anwar
Muhammad Hamza
Muhammad Musharaf
Tehmina Kiani
Faisal Nouroz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1526566

1,874 views

Technology and Code

Published on 06 Jun 2025

DeepPredict: a state-of-the-art web server for protein secondary structure and relative solvent accessibility prediction

in Protein Bioinformatics

Wafa Alanazi
Di Meng
Gianluca Pollastri

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1607402

2,078 views

Original Research

Published on 14 Apr 2025

Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio

in Protein Bioinformatics

Ibukun John Abulude
Isabel Cristina Rodríguez Luna
Alejandro Sánchez Varela
Andrew Camilli
Daniel E. Kadouri
Xianwu Guo

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566486

4,865 views
3 citations

Original Research

Published on 25 Mar 2025

Molecular dynamic simulations to assess the structural variability of ClpV from Enterobacter cloacae

in Protein Bioinformatics

Tehrim Motiwala
Babalwa Nyide
Thandeka Khoza

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1498916

1,553 views

Mini Review

Published on 03 Feb 2025

Machine learning approaches for predicting protein-ligand binding sites from sequence data

in Protein Bioinformatics

Orhun Vural
Leon Jololian

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1520382

4,988 views
3 citations

Original Research

Published on 28 Jan 2025

Integrated bioinformatics analysis to explore potential therapeutic targets and drugs for small cell carcinoma of the esophagus

in Protein Bioinformatics

Maofei Zhu
Yueming Chu
Qiang Yuan
Junfeng Li
Silin Chen
Lin Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1495052

3,440 views
3 citations