Frontiers in Bioinformatics | Protein Bioinformatics

Original Research

Published on 18 Nov 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 Dcunha
Athira Perunelly Gopalakrishnan
Amal Fahma
Neelam Krishna
Altaf Mahin
Samseera Ummar
Prathik Basthikoppa Shivamurthy
Inamul Hasan Madar
Rajesh Raju

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1683469

668 views

Original Research

Accepted on 07 Nov 2025

Beyond Tanimoto: A Learned Bioactivity Similarity Index Enhances Ligand Discovery

in Protein Bioinformatics

Gustavo Schottlender
Juan Manuel Prieto
Marcelo Adrian Marti
Dario Fernández Do Porto

Frontiers in Bioinformatics

258 views

Original Research

Published on 05 Nov 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

736 views

Editorial

Published on 31 Oct 2025

Editorial: Computational protein function prediction based on sequence and/or structural data

in Protein Bioinformatics

Yaan J. Jang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1705252

849 views

Technology and Code

Accepted on 27 Oct 2025

Bacteriocin Prediction Through Cross-Validation-Based and Hypergraph-Based Feature Evaluation Approaches

in Protein Bioinformatics

Suraiya Akhter
John Miller

Frontiers in Bioinformatics

257 views

Original Research

Published on 24 Oct 2025

Unraveling the molecular basis of snake venom nerve growth factor: human TrkA recognition through molecular dynamics simulation and comparison with human nerve growth factor

in Protein Bioinformatics

Shrudhi Devi
Gurunathan Jayaraman

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1674791

694 views

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

1,233 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

635 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

2,354 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

1,096 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

2,234 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

1,610 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

2,241 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

2,075 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

2,381 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

5,248 views
4 citations