Methods

Published on 10 Oct 2023

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

in Biological Modeling and Simulation

Fabian Krause
Karsten Voigt
Barbara Di Ventura
Mehmet Ali Öztürk

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1243970

6,402 views
2 citations

Original Research

Published on 28 Sep 2023

AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study

in Biological Modeling and Simulation

Paul Arras
Han Byul Yoo
Lukas Pekar
Thomas Clarke
Lukas Friedrich
Christian Schröter
Jennifer Schanz
Jason Tonillo
Vanessa Siegmund
Achim Doerner

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1249247

9,838 views
7 citations

Original Research

Published on 27 Sep 2023

Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping

in Biological Modeling and Simulation

Masaud Shah
Hyun Goo Woo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1236617

1,673 views
2 citations

Original Research

Published on 20 Sep 2023

Unleashing Nature’s potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

in Biological Modeling and Simulation

Soukayna Baammi
Achraf El Allali
Rachid Daoud

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1227643

3,237 views
5 citations

Original Research

Published on 18 Sep 2023

Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope

in Biological Modeling and Simulation

Fabian C. Spoendlin
Brennan Abanades
Matthew I. J. Raybould
Wing Ki Wong
Guy Georges
Charlotte M. Deane

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1237621

4,244 views
12 citations

Original Research

Published on 18 Sep 2023

Hierarchical machine learning model predicts antimicrobial peptide activity against Staphylococcus aureus

in Biological Modeling and Simulation

Hosein Khabaz
Mehdi Rahimi-Nasrabadi
Amir Homayoun Keihan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1238509

1,638 views
1 citation

Original Research

Published on 18 Sep 2023

Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes

in Biological Modeling and Simulation

Beste Ozaydin
Carles Curutchet

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1268278

1,325 views

Original Research

Published on 24 Aug 2023

Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold

in Biological Modeling and Simulation

Francis Gaudreault
Jason Baardsnes
Yuliya Martynova
Aurore Dachon
Hervé Hogues
Christopher R. Corbeil
Enrico O. Purisima
Mélanie Arbour
Traian Sulea

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1253689

2,064 views
1 citation

Original Research

Published on 10 Aug 2023

Anti-quorum sensing potential of selenium nanoparticles against LasI/R, RhlI/R, and PQS/MvfR in Pseudomonas aeruginosa: a molecular docking approach

in Biological Modeling and Simulation

Kanak Raj Kanak
Regina Sharmila Dass
Archana Pan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1203672

4,024 views
9 citations

Original Research

Published on 10 Aug 2023

Genetic analysis of acute intermittent porphyria caused by novel classical splicing variant in the insertion region of 29-residue specific to human HMBS protein

in Biological Modeling and Simulation

Lei Liang
Haixia Meng
Haotian Wu
Jianrong Zhao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1230798

2,102 views

Original Research

Published on 09 Aug 2023

In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria

in Biological Modeling and Simulation

Harpreet Singh
Shaikha Y. Almaazmi
Tanima Dutta
Robert A. Keyzers
Gregory L. Blatch

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1158912

3,915 views
4 citations

Review

Published on 07 Aug 2023

How can we discover developable antibody-based biotherapeutics?

in Biological Modeling and Simulation

Joschka Bauer
Nandhini Rajagopal
Priyanka Gupta
Pankaj Gupta
Andrew E. Nixon
Sandeep Kumar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1221626

7,852 views
12 citations

Original Research

Published on 04 Aug 2023

Machine learning-driven exploration of drug therapies for triple-negative breast cancer treatment

in Biological Modeling and Simulation

Aman Chandra Kaushik
Zhongming Zhao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1215204

2,685 views

Hypothesis and Theory

Published on 25 Jul 2023

Integrated immunoinformatics and subtractive proteomics approach for multi-epitope vaccine designing to combat S. pneumoniae TIGR4

in Biological Modeling and Simulation

Sami S. Ashgar
Hani Faidah
Farkad Bantun
Naif A. Jalal
Naeem F. Qusty
Abdulla Darwish
Shafiul Haque
Essam M. Janahi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1212119

5,884 views
3 citations

Original Research

Published on 14 Jul 2023

A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs

in Biological Modeling and Simulation

Venkat R. Pannala
Hung D. Nguyen
Anders Wallqvist

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1100434

1,646 views

Review

Published on 11 Jul 2023

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs

in Biological Modeling and Simulation

Zeyaul Islam
Pankaj Kumar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1228763

2,812 views
3 citations

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Articles

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study

Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping

Unleashing Nature’s potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope

Hierarchical machine learning model predicts antimicrobial peptide activity against Staphylococcus aureus

Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes

Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold

Anti-quorum sensing potential of selenium nanoparticles against LasI/R, RhlI/R, and PQS/MvfR in Pseudomonas aeruginosa: a molecular docking approach

Genetic analysis of acute intermittent porphyria caused by novel classical splicing variant in the insertion region of 29-residue specific to human HMBS protein

In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria

How can we discover developable antibody-based biotherapeutics?

Machine learning-driven exploration of drug therapies for triple-negative breast cancer treatment

Integrated immunoinformatics and subtractive proteomics approach for multi-epitope vaccine designing to combat S. pneumoniae TIGR4

A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs