Frontiers in Bioinformatics | Protein Bioinformatics

Original Research

Published on 17 Nov 2022

Nearest neighbor search on embeddings rapidly identifies distant protein relations

in Protein Bioinformatics

Konstantin Schütze
Michael Heinzinger
Martin Steinegger
Burkhard Rost

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1033775

6,371 views
30 citations

Perspective

Published on 21 Oct 2022

Towards rational computational peptide design

in Protein Bioinformatics

Liwei Chang
Arup Mondal
Alberto Perez

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1046493

8,327 views
26 citations

Original Research

Published on 10 Oct 2022

SETH predicts nuances of residue disorder from protein embeddings

in Protein Bioinformatics

Dagmar Ilzhöfer
Michael Heinzinger
Burkhard Rost

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1019597

5,185 views
37 citations

Perspective

Published on 07 Oct 2022

Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy

in Protein Bioinformatics

Priscila S. F. C. Gomes
Diego E. B. Gomes
Rafael C. Bernardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.983306

10,692 views
25 citations

Original Research

Published on 30 Sep 2022

In silico discovery of biomarkers for the accurate and sensitive detection of Fusarium solani

in Protein Bioinformatics

Olalekan Olanrewaju Bakare
Arun Gokul
Muhali Olaide Jimoh
Ashwil Klein
Marshall Keyster

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.972529

2,953 views
1 citation

Original Research

Published on 26 Sep 2022

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

in Protein Bioinformatics

Isak Johansson-Åkhe
Björn Wallner

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.959160

30,953 views
120 citations

Original Research

Published on 23 Jun 2022

A Machine Learning Framework Predicts the Clinical Severity of Hemophilia B Caused by Point-Mutations

in Protein Bioinformatics

Tiago J. S. Lopes
Tatiane Nogueira
Ricardo Rios

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.912112

5,036 views
9 citations

Original Research

Published on 21 Jun 2022

Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93

in Protein Bioinformatics

Vittoria Cicaloni
Malancha Karmakar
Luisa Frusciante
Francesco Pettini
Anna Visibelli
Maurizio Orlandini
Federico Galvagni
Maurizio Mongiat
Michael Silk
Federica Nardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.891553

2,770 views
3 citations

Original Research

Published on 02 Jun 2022

ContactPFP: Protein Function Prediction Using Predicted Contact Information

in Protein Bioinformatics

Yuki Kagaya
Sean T. Flannery
Aashish Jain
Daisuke Kihara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.896295

41,772 views
9 citations

Original Research

Published on 27 May 2022

Darwinian Evolution of Intelligence

in Protein Bioinformatics

J. C. Phillips

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.838420

1,976 views

Review

Published on 19 May 2022

Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics

in Protein Bioinformatics

Kenta Nakai
Leyi Wei

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.910531

7,836 views
10 citations

Original Research

Published on 05 May 2022

Mimetic Neural Networks: A Unified Framework for Protein Design and Folding

in Protein Bioinformatics

Moshe Eliasof
Tue Boesen
Eldad Haber
Chen Keasar
Eran Treister

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.715006

4,660 views
9 citations

Original Research

Published on 18 Feb 2022

BERT-Kgly: A Bidirectional Encoder Representations From Transformers (BERT)-Based Model for Predicting Lysine Glycation Site for Homo sapiens

in Protein Bioinformatics

Yinbo Liu
Yufeng Liu
Gang-Ao Wang
Yinchu Cheng
Shoudong Bi
Xiaolei Zhu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.834153

5,503 views
19 citations

Original Research

Published on 02 Dec 2021

BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins

in Protein Bioinformatics

Sankar Basu
Simon S. Assaf
Fabian Teheux
Marianne Rooman
Fabrizio Pucci

Frontiers in Bioinformatics

doi 10.3389/fbinf.2021.742843

3,114 views
5 citations

Original Research

Published on 03 Nov 2021

A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks

in Protein Bioinformatics

Yongcheng Mu
Salim Sazzed
Maytha Alshammari
Jiangwen Sun
Jing He

Frontiers in Bioinformatics

doi 10.3389/fbinf.2021.710119

5,083 views
14 citations

Methods

Published on 25 Oct 2021

InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network

in Protein Bioinformatics

Isak Johansson-Åkhe
Claudio Mirabello
Björn Wallner

Frontiers in Bioinformatics

doi 10.3389/fbinf.2021.763102

5,946 views
15 citations