Frontiers in Bioinformatics | Protein Bioinformatics

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

189 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

1,514 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

759 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

1,801 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

1,298 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

1,866 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

1,642 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

1,898 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

4,577 views
1 citation

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

1,463 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

4,606 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

3,251 views
2 citations

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

1,470 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

11,079 views
1 citation

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

2,693 views
3 citations

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

3,601 views
1 citation