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Decomposition of Small Molecules for Fragment-Based Drug Design

JOURNAL ARTICLE published 24 May 2023 in Biophysica

Research funded by Russian Science Foundation (22-23-00729)

Authors: Nikita N. Ivanov | Dmitry A. Shulga | Vladimir A. Palyulin

https://doi.org/10.3390/biophysica3020024 Actions

The Dynamic Behavior of a Single Semiflexible Ring Chain in a Linear Polymer Matrix

JOURNAL ARTICLE published 26 July 2023 in Biophysica

Research funded by Fundamental Research Funds for the Central Universities (3072021CFT2508) | National Defense Basic Research Program of China (JCKYS2023604SSJS003) | Fundamental Research Funds of Harbin Engineering University (3072023CFJ2501)

Authors: Xiaolin Zhou | Yifan Qin

https://doi.org/10.3390/biophysica3030031 Actions

Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen

JOURNAL ARTICLE published 2 April 2023 in Biophysica

Research funded by Russian Science Foundation (22-13-00012)

Authors: Igor Polyakov | Anna Kulakova | Alexander Nemukhin

https://doi.org/10.3390/biophysica3020016 Actions

A Structure-Guided Designed Small Molecule Is an Anticancer Agent and Inhibits the Apoptosis-Related MCL-1 Protein

JOURNAL ARTICLE published 7 July 2023 in Biophysica

Research funded by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (001)

Authors: Ingrid V. Machado | Luiz F. N. Naves | Jean M. F. Custodio | Hérika D. A. Vidal | Jaqueline E. Queiroz | Allen G. Oliver | Joyce V. B. Borba | Bruno J. Neves | Lucas M. Brito | Claudia Pessoa | Hamilton B. Napolitano | Gilberto L. B. de Aquino

https://doi.org/10.3390/biophysica3030029 Actions

Physicochemical Characterization of the Catalytic Unit of Hammerhead Ribozyme and Its Relationship with the Catalytic Activity

JOURNAL ARTICLE published 25 August 2022 in Biophysica

Research funded by International Human Frontier Science Program Organization (RGY0082/2008-C) | Ministry of Education, Culture, Sports, Science and Technology (22K05320, 19K05705 20550145 and 24310163)

Authors: Yoshiyuki Tanaka | Daichi Yamanaka | Saori Morioka | Taishi Yamaguchi | Masayuki Morikawa | Takashi S. Kodama | Vladimír Sychrovský | Chojiro Kojima | Yoshikazu Hattori

https://doi.org/10.3390/biophysica2030022 Actions

Molecular Forces Governing the Biological Function of Per-Arnt-Sim-B (PAS-B) Domains: A Comparative Computational Study

JOURNAL ARTICLE published 5 February 2021 in Biophysica

Research funded by EPSRC (EP/S022791/1)

Authors: João Victor de Souza | Piotr Zaborniak | Sylvia Reznikov | Matthew Kondal | Ruidi Zhu | Agnieszka K. Bronowska

https://doi.org/10.3390/biophysica1010001 Actions

Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques

JOURNAL ARTICLE published 30 March 2021 in Biophysica

Research funded by National Science Foundation (1807131) | National Institute of General Medical Sciences (R35 GM126935)

Authors: Indra D. Sahu | Gary A. Lorigan

https://doi.org/10.3390/biophysica1020009 Actions

Present and Future Opportunities in Imaging the Ubiquitin System (Ub-System)

JOURNAL ARTICLE published 28 July 2022 in Biophysica

Authors: Leonardo Mortati | Barbara Pergolizzi | Cristina Panuzzo | Enrico Bracco

https://doi.org/10.3390/biophysica2030018 Actions

Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations

JOURNAL ARTICLE published 8 April 2021 in Biophysica

Authors: Christos T. Chasapis | Alexios Vlamis-Gardikas

https://doi.org/10.3390/biophysica1020012 Actions

Structural Insights into Plasticity and Discovery of Flavonoid Allosteric Inhibitors of Flavivirus NS2B–NS3 Protease

JOURNAL ARTICLE published 1 February 2023 in Biophysica

Research funded by São Paulo Research Foundation (2013/21719-3,2020/12875-5) | National Institutes of Health (U01AI151807) | Coordenação de Aperfeicoamento de Pessoal de Nível Superior (88887.659079/2021-00)

Authors: Marielena Vogel Saivish | Gabriela de Lima Menezes | Vivaldo Gomes da Costa | Liliane Nebo | Gislaine Celestino Dutra da Silva | Carolina Colombelli Pacca | Rafael Elias Marques | Maurício Lacerda Nogueira | Roosevelt Alves Da Silva

https://doi.org/10.3390/biophysica3010006 Actions

Old Enzyme, New Role: The β-Glucosidase BglC of Streptomyces scabiei Interferes with the Plant Defense Mechanism by Hydrolyzing Scopolin

JOURNAL ARTICLE published 22 December 2021 in Biophysica

Research funded by Fund for Scientific Research (grant 1.A618.18,grant CDR/OL J.0158.21)

Authors: Benoit Deflandre | Sébastien Rigali

https://doi.org/10.3390/biophysica2010001 Actions

Probing Biochemical Differences in Lipid Components of Human Cells by Means of ATR-FTIR Spectroscopy

JOURNAL ARTICLE published 1 September 2023 in Biophysica

Authors: Marianna Portaccio | Bahar Faramarzi | Maria Lepore

https://doi.org/10.3390/biophysica3030035 Actions

Binding Constants of Clinical Drugs and Other Organic Ligands with Human and Mammalian Serum Albumins

JOURNAL ARTICLE published 8 September 2021 in Biophysica

Research funded by Russian Science Foundation (19-73-00209)

Authors: Igor Sedov | Alena Nikiforova | Diliara Khaibrakhmanova

https://doi.org/10.3390/biophysica1030026 Actions

Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography

JOURNAL ARTICLE published 11 April 2023 in Biophysica

Research funded by European Union (101046651)

Authors: Giovanni Novi Inverardi | Francesco Carnovale | Lorenzo Petrolli | Simone Taioli | Gianluca Lattanzi

https://doi.org/10.3390/biophysica3020018 Actions

Insights into the Substrate Uptake Mechanism of Mycobacterium Tuberculosis Ribose 5-Phosphate Isomerase and Perspectives on Drug Development

JOURNAL ARTICLE published 1 March 2023 in Biophysica

Research funded by FAPERJ (239229,215141,204432,225356) | CDAB and CNPq (309564/2017-4) | FAPERJ (202280)

Authors: Leonardo Bartkevihi | Ícaro P. Caruso | Bruna Martins | José R. M. Pires | Danielle M. P. Oliveira | Cristiane Dinis Anobom | Fabio C. L. Almeida

https://doi.org/10.3390/biophysica3010010 Actions

SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules

JOURNAL ARTICLE published 19 May 2021 in Biophysica

Research funded by Monash University (NA,DE210101479,MRFF COVID-19,SRF #1159272) | Australian Nuclear Science and Technology Organisation (AINSE ECR grant)

Authors: Andrea T. Nguyen | Christopher Szeto | Dhilshan Jayasinghe | Christian A. Lobos | Hanim Halim | Demetra S. M. Chatzileontiadou | Emma J. Grant | Stephanie Gras

https://doi.org/10.3390/biophysica1020015 Actions

Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers

JOURNAL ARTICLE published 28 February 2024 in Biophysica

Research funded by Generalitat de Catalunya (2021SGR00350) | Spanish Structures of Excellence María de Maeztu program (CEX2021-001202-M) | Spanish Ministry of Science and Innovation (PID2022-140312NB-C21) | European Union’s Horizon Europe research and innovation programme (101062456)

Authors: David Naranjo | Pablo M. Blanco | Josep L. Garcés | Sergio Madurga | Francesc Mas

https://doi.org/10.3390/biophysica4010008 Actions

Effects of Ionic Liquids on Laccase from Trametes versicolor

JOURNAL ARTICLE published 20 October 2021 in Biophysica

Research funded by National Science Foundation (DMR 1904797) | Extreme Science and Engineering Discovery Environment (MCB 170088,PSCA17017P)

Authors: Aashka Y. Patel | Austin K. Clark | Nicholas J. Paradis | Meeraj Amin | Timothy D. Vaden | Chun Wu | Gregory A. Caputo

https://doi.org/10.3390/biophysica1040031 Actions

Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer

JOURNAL ARTICLE published 14 May 2021 in Biophysica

Research funded by Council for Grants of the President of the Russian Federation (SP-1680.2018.4)

Authors: Gleb Zhdanov | Alexander Arutyunyuan | Alexey Kopylov | Elena Zavyalova

https://doi.org/10.3390/biophysica1020014 Actions

Effect of the Neck Linker on Processive Stepping of Kinesin Motor

JOURNAL ARTICLE published 28 January 2023 in Biophysica

Authors: Ping Xie

https://doi.org/10.3390/biophysica3010004 Actions
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