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Machine learning in the prediction of cancer therapy

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Authors: Raihan Rafique | S.M. Riazul Islam | Julhash U. Kazi

New insights into the acetate uptake transporter (AceTr) family: Unveiling amino acid residues critical for specificity and activity

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Authors: Toni Rendulić | João Alves | João Azevedo-Silva | Isabel Soares-Silva | Margarida Casal

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Authors: Sara Benito-Vaquerizo | Martijn Diender | Ivette Parera Olm | Vitor A.P. Martins dos Santos | Peter J. Schaap | Diana Z. Sousa | Maria Suarez-Diez

The impact of pathogenic and artificial mutations on Claudin-5 selectivity from molecular dynamics simulations

JOURNAL ARTICLE published 2023 in Computational and Structural Biotechnology Journal

Authors: Alessandro Berselli | Giulio Alberini | Fabio Benfenati | Luca Maragliano

Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Rita Padányi | Bianka Farkas | Hedvig Tordai | Bálint Kiss | Helmut Grubmüller | Naoto Soya | Gergely L. Lukács | Miklós Kellermayer | Tamás Hegedűs

AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Authors: Binbin Xi | Zixi Chen | Shuhua Li | Wei Liu | Dawei Jiang | Yunmeng Bai | Yimo Qu | Jerome Rumdon Lon | Lizhen Huang | Hongli Du

A rapid CRISPR competitive assay for in vitro and in vivo discovery of potential drug targets affecting the hematopoietic system

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Authors: Yunbing Shen | Long Jiang | Vaishnavi Srinivasan Iyer | Bruno Raposo | Anatoly Dubnovitsky | Sanjaykumar V. Boddul | Zsolt Kasza | Fredrik Wermeling

Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Research funded by Sapienza Università di Roma (GA116154C8A94E3D,RG11816430AF48E1,RM11715C646D693E,RM11916B46D48441,RM120172A7AD98EB) | Associazione Italiana per la Ricerca sul Cancro (IG2019-ID23125) | Horizon 2020 Framework Programme (IASIS 727658,INFORE 25080) | European Research Council (ASTRA 855923,RIBOMYLOME 309545) | Ministerio de Economía y Competitividad (BFU2017-86970-P)

Authors: Michele Monti | Giulia Guiducci | Alessio Paone | Serena Rinaldo | Giorgio Giardina | Francesca Romana Liberati | Francesca Cutruzzolá | Gian Gaetano Tartaglia

Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Research funded by National Science Foundation (DBI2030790,IIS1901191) | National Institute of General Medical Sciences (GM136422,S10OD026825) | National Institute of Allergy and Infectious Diseases (AI081062,AI134678)

Authors: Edison Ong | Xiaoqiang Huang | Robin Pearce | Yang Zhang | Yongqun He

Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Research funded by Department of Science and Technology, Ministry of Science and Technology, India (GAP362) | Council of Scientific and Industrial Research, India (GAP362) | CSIR-Indian Institute of Chemical Biology (GAP362)

Authors: Ishita Mukherjee | Saikat Chakrabarti

D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Suchetana Gupta | Ditipriya Mallick | Kumarjeet Banerjee | Shrimon Mukherjee | Soumyadev Sarkar | Sonny TM Lee | Partha Basuchowdhuri | Siddhartha S Jana

Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Research funded by US Department of Defense Prostate Cancer Research Program (W81XWH-18-1-0189) | Department of Science and Technology, Ministry of Science and Technology, India (SB/S2/RJN-049/2018) | National Cancer Institute (1R01CA233585-02)

Authors: Priyanka Chakraborty | Emily L. Chen | Isabelle McMullen | Andrew J. Armstrong | Mohit Kumar Jolly | Jason A. Somarelli

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: Insights from an agent-based model

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Research funded by Medical Research Council (MR/N021444/1) | Engineering and Physical Sciences Research Council (EP/R041695/1,EP/S01876X/1) | European Commission (766840)

Authors: Daniel Ward | Sandra Montes Olivas | Alexander Fletcher | Martin Homer | Lucia Marucci

Unraveling membrane properties at the organelle-level with LipidDyn

JOURNAL ARTICLE published 2022 in Computational and Structural Biotechnology Journal

Authors: Simone Scrima | Matteo Tiberti | Alessia Campo | Elisabeth Corcelle-Termeau | Delphine Judith | Mads Møller Foged | Knut Kristoffer Bundgaard Clemmensen | Sharon A. Tooze | Marja Jäättelä | Kenji Maeda | Matteo Lambrughi | Elena Papaleo

MOSGA 2: Comparative genomics and validation tools

JOURNAL ARTICLE published 2021 in Computational and Structural Biotechnology Journal

Authors: Roman Martin | Hagen Dreßler | Georges Hattab | Thomas Hackl | Matthias G. Fischer | Dominik Heider

Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1

JOURNAL ARTICLE published 2019 in Computational and Structural Biotechnology Journal

Research funded by National Institutes of Health (K99HL135442,R35GM127087,HL122010,P50GM115305)

Authors: Brett M. Kroncke | Jeffrey Mendenhall | Derek K. Smith | Charles R. Sanders | John A. Capra | Alfred L. George | Jeffrey D. Blume | Jens Meiler | Dan M. Roden

A drug repurposing method based on inhibition effect on gene regulatory network

JOURNAL ARTICLE published 2023 in Computational and Structural Biotechnology Journal

Authors: Xianbin Li | Minzhen Liao | Bing Wang | Xiangzhen Zan | Yanhao Huo | Yue Liu | Zhenshen Bao | Peng Xu | Wenbin Liu

Method development for cross-study microbiome data mining: Challenges and opportunities

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Authors: Xiaoquan Su | Gongchao Jing | Yufeng Zhang | Shunyao Wu

Mitotic chromosome organization: General rules meet species-specific variability

JOURNAL ARTICLE published 2020 in Computational and Structural Biotechnology Journal

Authors: Tomáš Beseda | Petr Cápal | Ivona Kubalová | Veit Schubert | Jaroslav Doležel | Hana Šimková

Epigenetic modifications: Allusive clues of lncRNA functions in plants

JOURNAL ARTICLE published 2023 in Computational and Structural Biotechnology Journal

Authors: Wenjing Yang | Quanzi Bai | Yan Li | Jianghua Chen | Changning Liu