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Computational approaches to understand transcription regulation in development

Maarten van der Sande, Siebren Frölich, Simon J. van Heeringen

Biochem Soc Trans (2023) BST20210145.

DOI: https://doi.org/10.1042/BST20210145

Published: 25 January 2023

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Articles

Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology

Steven Turner, Jonathan W. Essex, Tim Elliott

Biochem Soc Trans (2023) BST20220782.

DOI: https://doi.org/10.1042/BST20220782

Published: 16 January 2023

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Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features

Helena García-Castro, Jordi Solana

Biochem Soc Trans (2022) 50 (5): 1237–1246.

DOI: https://doi.org/10.1042/BST20210825

Published: 25 October 2022

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Articles

Effects of antibiotics on bacterial cell morphology and their physiological origins

Callaghan Cylke, Fangwei Si, Shiladitya Banerjee

Biochem Soc Trans (2022) 50 (5): 1269–1279.

DOI: https://doi.org/10.1042/BST20210894

Published: 12 September 2022

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Articles

Drug repurposing in silico screening platforms

Jonathan G.L. Mullins

Biochem Soc Trans (2022) 50 (2): 747–758.

DOI: https://doi.org/10.1042/BST20200967

Published: 14 March 2022

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Articles

Phenomics approaches to understand genetic networks and gene function in yeast

Clarence Hue Lok Yeung, Nil Sahin, Brenda Andrews

Biochem Soc Trans (2022) 50 (2): 713–721.

DOI: https://doi.org/10.1042/BST20210285

Published: 14 March 2022

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Articles

Exploring cryo-electron microscopy with molecular dynamics

John W. Vant, Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, Abhishek Singharoy

Biochem Soc Trans (2022) 50 (1): 569–581.

DOI: https://doi.org/10.1042/BST20210485

Published: 25 February 2022

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Articles

Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data

Suoqin Jin, Raul Ramos

Biochem Soc Trans (2022) 50 (1): 297–308.

DOI: https://doi.org/10.1042/BST20210863

Published: 22 February 2022

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Articles

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

F. Emil Thomasen, Kresten Lindorff-Larsen

Biochem Soc Trans (2022) 50 (1): 541–554.

DOI: https://doi.org/10.1042/BST20210499

Published: 07 February 2022

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Articles

Big data and artificial intelligence (AI) methodologies for computer-aided drug design (CADD)

Jai Woo Lee, Miguel A. Maria-Solano, Thi Ngoc Lan Vu, Sanghee Yoon, Sun Choi

Biochem Soc Trans (2022) 50 (1): 241–252.

DOI: https://doi.org/10.1042/BST20211240

Published: 25 January 2022

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Articles

Computational methods to study enveloped viral entry

Alzbeta Tuerkova, Peter M. Kasson

Biochem Soc Trans (2021) 49 (6): 2527–2537.

DOI: https://doi.org/10.1042/BST20210190

Published: 16 November 2021

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Includes: Supplementary data

Articles

Progress and challenges in understanding the regulation and function of p53 dynamics

Zhilin Yang, Ryan L. Hanson, Eric Batchelor

Biochem Soc Trans (2021) 49 (5): 2123–2131.

DOI: https://doi.org/10.1042/BST20210148

Published: 08 September 2021

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Articles

Polymer models are a versatile tool to study chromatin 3D organization

Andrea Esposito, Simona Bianco, Luca Fiorillo, Mattia Conte, Alex Abraham, Francesco Musella, Mario Nicodemi, Antonella Prisco, Andrea M. Chiariello

Biochem Soc Trans (2021) 49 (4): 1675–1684.

DOI: https://doi.org/10.1042/BST20201004

Published: 20 July 2021

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Articles

Quantitative neurogenetics: applications in understanding disease

Ali Afrasiabi, Jeremy T. Keane, Julian Ik-Tsen Heng, Elizabeth E. Palmer, Nigel H. Lovell, Hamid Alinejad-Rokny

Biochem Soc Trans (2021) 49 (4): 1621–1631.

DOI: https://doi.org/10.1042/BST20200732

Published: 20 July 2021

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Articles

The view of microbes as energy converters illustrates the trade-off between growth rate and yield

St. Elmo Wilken, Victor Vera Frazão, Nima P. Saadat, Oliver Ebenhöh

Biochem Soc Trans (2021) 49 (4): 1663–1674.

DOI: https://doi.org/10.1042/BST20200977

Published: 20 July 2021

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Articles

Structural dynamics of ABC transporters: molecular simulation studies

Tadaomi Furuta

Biochem Soc Trans (2021) 49 (1): 405–414.

DOI: https://doi.org/10.1042/BST20200710

Published: 26 February 2021

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Articles

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

Cecilia Lövkvist, Martin Howard

Biochem Soc Trans (2021) 49 (1): 71–77.

DOI: https://doi.org/10.1042/BST20190955

Published: 22 February 2021

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Articles

One-carbon metabolism in cancer cells: a critical review based on a core model of central metabolism

Jean-Pierre Mazat

Biochem Soc Trans (2021) 49 (1): 1–15.

DOI: https://doi.org/10.1042/BST20190008

Published: 22 February 2021

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Includes: Supplementary data

Articles

Computational investigations of allostery in aromatic amino acid biosynthetic enzymes

Wanting Jiao

Biochem Soc Trans (2021) 49 (1): 415–429.

DOI: https://doi.org/10.1042/BST20200741

Published: 05 February 2021

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Articles

Finding new edges: systems approaches to MTOR signaling

Alexander Martin Heberle, Ulrike Rehbein, Maria Rodríguez Peiris, Kathrin Thedieck

Biochem Soc Trans (2021) 49 (1): 41–54.

DOI: https://doi.org/10.1042/BST20190730

Published: 05 February 2021

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Articles

Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis

Jocelyn A. Hammond, Emma A. Gordon, Kayla M. Socarras, Joshua Chang Mell, Garth D. Ehrlich

Biochem Soc Trans (2020) 48 (6): 2437–2455.

DOI: https://doi.org/10.1042/BST20190713

Published: 27 November 2020

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Articles

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

Fernando Cruz, José P. Faria, Miguel Rocha, Isabel Rocha, Oscar Dias

Biochem Soc Trans (2020) 48 (5): 1889–1903.

DOI: https://doi.org/10.1042/BST20190840

Published: 17 September 2020

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Includes: Supplementary data

Articles

A brief note on the properties of linear pathways

Herbert M. Sauro

Biochem Soc Trans (2020) 48 (4): 1379–1395.

DOI: https://doi.org/10.1042/BST20190842

Published: 24 August 2020

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Articles

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners

Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco

Biochem Soc Trans (2020) 48 (4): 1529–1543.

DOI: https://doi.org/10.1042/BST20191059

Published: 21 August 2020

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Articles

Modeling the nucleoporins that form the hairy pores

Kai Huang, Igal Szleifer

Biochem Soc Trans (2020) 48 (4): 1447–1461.

DOI: https://doi.org/10.1042/BST20190941

Published: 14 August 2020

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Articles

Plant transporters involved in combating boron toxicity: beyond 3D structures

Maria Hrmova, Matthew Gilliham, Stephen D. Tyerman

Biochem Soc Trans (2020) 48 (4): 1683–1696.

DOI: https://doi.org/10.1042/BST20200164

Published: 11 August 2020

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Articles

Computational methods for exploring protein conformations

Jane R. Allison

Biochem Soc Trans (2020) 48 (4): 1707–1724.

DOI: https://doi.org/10.1042/BST20200193

Published: 05 August 2020

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Articles

Reinforcement learning in synthetic gene circuits

Adrian Racovita, Alfonso Jaramillo

Biochem Soc Trans (2020) 48 (4): 1637–1643.

DOI: https://doi.org/10.1042/BST20200008

Published: 05 August 2020

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Articles

Genome scale metabolic models and analysis for evaluating probiotic potentials

Yoon-Mi Choi, Yi Qing Lee, Hyun-Seob Song, Dong-Yup Lee

Biochem Soc Trans (2020) 48 (4): 1309–1321.

DOI: https://doi.org/10.1042/BST20190668

Published: 29 July 2020

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Articles

The mitochondrial ADP/ATP carrier exists and functions as a monomer

Edmund R.S. Kunji, Jonathan J. Ruprecht

Biochem Soc Trans (2020) 48 (4): 1419–1432.

DOI: https://doi.org/10.1042/BST20190933

Published: 29 July 2020

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Articles

Computational discovery and modeling of novel gene expression rules encoded in the mRNA

Shir Bahiri-Elitzur, Tamir Tuller

Biochem Soc Trans (2020) 48 (4): 1519–1528.

DOI: https://doi.org/10.1042/BST20191048

Published: 14 July 2020

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Articles

Structural predictions of the functions of membrane proteins from HDX-MS

Andy M. Lau, Ruyu Jia, Richard T. Bradshaw, Argyris Politis

Biochem Soc Trans (2020) 48 (3): 971–979.

DOI: https://doi.org/10.1042/BST20190880

Published: 29 June 2020

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Articles

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Clémence Frioux, Simon M. Dittami, Anne Siegel

Biochem Soc Trans (2020) 48 (3): 901–913.

DOI: https://doi.org/10.1042/BST20190667

Published: 07 May 2020

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Articles

Towards the routine use of in silico screenings for drug discovery using metabolic modelling

Tamara Bintener, Maria Pires Pacheco, Thomas Sauter

Biochem Soc Trans (2020) 48 (3): 955–969.

DOI: https://doi.org/10.1042/BST20190867

Published: 05 May 2020

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Includes: Supplementary data

Articles

Mathematical modelling in cell migration: tackling biochemistry in changing geometries

Björn Stinner, Till Bretschneider

Biochem Soc Trans (2020) 48 (2): 419–428.

DOI: https://doi.org/10.1042/BST20190311

Published: 02 April 2020

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Articles

Visualizing protein structures — tools and trends

Xavier Martinez, Matthieu Chavent, Marc Baaden

Biochem Soc Trans (2020) 48 (2): 499–506.

DOI: https://doi.org/10.1042/BST20190621

Published: 20 March 2020

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Articles

The energetics of protein–lipid interactions as viewed by molecular simulations

Robin A. Corey, Phillip J. Stansfeld, Mark S.P. Sansom

Biochem Soc Trans (2020) 48 (1): 25–37.

DOI: https://doi.org/10.1042/BST20190149

Published: 24 December 2019

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Articles

The role of ligand-gated conformational changes in enzyme catalysis

Cátia Moreira, Ana Rita Calixto, John P. Richard, Shina Caroline Lynn Kamerlin

Biochem Soc Trans (2019) 47 (5): 1449–1460.

DOI: https://doi.org/10.1042/BST20190298

Published: 28 October 2019

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Articles

Structural snapshots of RAF kinase interactions

Soheila Rezaei Adariani, Marcel Buchholzer, Mohammad Akbarzadeh, Saeideh Nakhaei-Rad, Radovan Dvorsky, Mohammad Reza Ahmadian

Biochem Soc Trans (2018) 46 (6): 1393–1406.

DOI: https://doi.org/10.1042/BST20170528

Published: 31 October 2018

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Includes: Supplementary data

Articles

Protein structure and computational drug discovery

Tracy L. Nero, Michael W. Parker, Craig J. Morton

Biochem Soc Trans (2018) 46 (5): 1367–1379.

DOI: https://doi.org/10.1042/BST20180202

Published: 21 September 2018

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Articles

Methods for automated genome-scale metabolic model reconstruction

José P. Faria, Miguel Rocha, Isabel Rocha, Christopher S. Henry

Biochem Soc Trans (2018) 46 (4): 931–936.

DOI: https://doi.org/10.1042/BST20170246

Published: 31 July 2018

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Articles

Thermodynamic constraints for identifying elementary flux modes

Sabine Peres, Stefan Schuster, Philippe Dague

Biochem Soc Trans (2018) 46 (3): 641–647.

DOI: https://doi.org/10.1042/BST20170260

Published: 09 May 2018

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Articles

Self-organization, entropy and allostery

Alexandr P. Kornev

Biochem Soc Trans (2018) 46 (3): 587–597.

DOI: https://doi.org/10.1042/BST20160144

Published: 20 April 2018

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Articles

Modelling phosphorus uptake in microalgae

Dipali Singh, Ladislav Nedbal, Oliver Ebenhöh

Biochem Soc Trans (2018) 46 (2): 483–490.

DOI: https://doi.org/10.1042/BST20170262

Published: 17 April 2018

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Articles

Exploring the combinatorial space of complete pathways to chemicals

Lin Wang, Chiam Yu Ng, Satyakam Dash, Costas D. Maranas

Biochem Soc Trans (2018) 46 (3): 513–522.

DOI: https://doi.org/10.1042/BST20170272

Published: 06 April 2018

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Articles

Review and perspective on mathematical modeling of microbial ecosystems

Antonella Succurro, Oliver Ebenhöh

Biochem Soc Trans (2018) 46 (2): 403–412.

DOI: https://doi.org/10.1042/BST20170265

Published: 14 March 2018

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Articles

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia

Ross P. Carlson, Ashley E. Beck, Poonam Phalak, Matthew W. Fields, Tomas Gedeon, Luke Hanley, William R. Harcombe, Michael A. Henson, Jeffrey J. Heys

Biochem Soc Trans (2018) 46 (2): 269–284.

DOI: https://doi.org/10.1042/BST20170242

Published: 22 February 2018

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Articles

Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function

Mehari B. Zerihun, Alexander Schug

Biochem Soc Trans (2017) 45 (6): 1253–1261.

DOI: https://doi.org/10.1042/BST20170063

Published: 20 October 2017

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Articles

Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances

Jan Ewald, Martin Bartl, Christoph Kaleta

Biochem Soc Trans (2017) 45 (4): 1035–1043.

DOI: https://doi.org/10.1042/BST20170137

Published: 28 July 2017

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Identification of optimal strategies for state transition of complex biological networks

Meichen Yuan, Weirong Hong, Pu Li

Biochem Soc Trans (2017) 45 (4): 1015–1024.

DOI: https://doi.org/10.1042/BST20160419

Published: 21 July 2017

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