M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

Authors: Cui, Xinyue¹ (AUTHOR) Cuixinyue@zjut.edu.cn, Xia, Yuhao¹ (AUTHOR) xiayh@zjut.edu.cn, Hou, Minghua¹ (AUTHOR) minghua@zjut.edu.cn, Zhao, Xuanfeng¹ (AUTHOR) 221122030319@zjut.edu.cn, Wang, Suhui¹ (AUTHOR) suhui@zjut.edu.cn, Zhang, Guijun¹ (AUTHOR) zgj@zjut.edu.cn

Source: BMC Bioinformatics. 5/5/2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: *PROTEIN structure prediction, *FEATURE extraction, *PROTEIN structure, *DRUG design, *PROTEIN models, *PROTEIN conformation

Expanding kinetoplastid genome annotation through protein structure comparison.

Authors: Trinidad-Barnech, Juan Manuel^1,2 (AUTHOR), Sotelo-Silveira, José^3,4 (AUTHOR), Do Porto, Darío Fernández^5,6 (AUTHOR), Smircich, Pablo^1,7 (AUTHOR) psmircich@fcien.edu.uy

Source: PLoS Pathogens. 4/21/2025, Vol. 21 Issue 4, p1-21. 21p.

Subject Terms: *PROTEIN structure prediction, *PROTEIN structure, *INSPECTION & review, *DATABASES, *KNOWLEDGE transfer

Exploring FAM13A-N-Myc interactions to uncover potential targets in MYCN-amplified neuroblastoma: a study of protein interactions and molecular dynamics simulations.

Authors: Yin, Hongli¹ (AUTHOR) yinhongli1992@outlook.com, Liu, Tianyi² (AUTHOR), Wu, Di¹ (AUTHOR), Li, Xiaolu¹ (AUTHOR), Li, Gen¹ (AUTHOR), Song, Weiwei³ (AUTHOR), Wang, Xiaodong⁴ (AUTHOR), Xin, Shan⁵ (AUTHOR) shan.xin@yale.edu, Liu, Yisu⁶ (AUTHOR) Sophie1liu@foxmail.com, Pan, Jian¹ (AUTHOR) panjian2008@163.com

Source: BMC Cancer. 3/14/2025, Vol. 25 Issue 1, p1-23. 23p.

Subject Terms: *PROTEIN structure prediction, *MACHINE learning, *MOLECULAR dynamics, *PROTEIN structure, *PROTEIN stability

Structure‐based virtual screening aids the identification of glycosyltransferases in the biosynthesis of salidroside.

Authors: Yao, Yan^1,2,3 (AUTHOR), Chen, Fangfang^1,2,3 (AUTHOR), Wu, Chaoyan¹ (AUTHOR), Chang, Xiaosa^1,2 (AUTHOR), Cheng, Weijia^1,2 (AUTHOR), Wang, Qiuxia^1,2 (AUTHOR), Deng, Zixin^1,2 (AUTHOR), Liu, Tiangang^1,2 (AUTHOR), Lu, Li^1,2,3 (AUTHOR) luliwhu@whu.edu.cn

Source: Plant Biotechnology Journal. May2025, Vol. 23 Issue 5, p1725-1735. 11p.

Subject Terms: *VIRTUAL high-throughput screening (Drug development), *PROTEIN structure prediction, *PLANT enzymes, *RUMEX, *GLYCOSYLTRANSFERASES

Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family in Marchantia polymorpha brings new insight into evolutionary developmental biology.

Authors: Zhou, Congye¹ (AUTHOR), Yang, Ting¹ (AUTHOR), Cai, Manlei¹ (AUTHOR), Cui, Hongchang² (AUTHOR), Yu, Fei¹ (AUTHOR), Liu, Huawei¹ (AUTHOR), Fu, Jing¹ (AUTHOR) jingfu@nwafu.edu.cn

Source: BMC Genomics. 4/29/2025, Vol. 26 Issue 1, p1-20. 20p.

Subject Terms: *PROTEIN structure prediction, *EVOLUTIONARY developmental biology, *CYTOLOGY, *LIFE sciences, *PLANT cells & tissues

Mycobacterium susceptibility to ivermectin by inhibition of eccD3, an ESX-3 secretion system component.

Authors: Granados-Tristán, Ana Laura^1,2 (AUTHOR), Carrillo-Tripp, Mauricio³ (AUTHOR), Hernández-Luna, Carlos Eduardo² (AUTHOR), Herrera-Rodulfo, Aldo³ (AUTHOR), González-Escalante, Laura Adiene¹ (AUTHOR), Arriaga-Guerrero, Ana Leticia^1,2 (AUTHOR), Silva-Ramírez, Beatriz⁴ (AUTHOR), Escobedo-Guajardo, Brenda Leticia¹ (AUTHOR), Mercado-Hernández, Roberto² (AUTHOR), Bermúdez de León, Mario¹ (AUTHOR), Peñuelas-Urquides, Katia¹ (AUTHOR) katia.penuelasu@imss.gob.mx

Source: PLoS Computational Biology. 4/17/2025, Vol. 21 Issue 4, p1-27. 27p.

Subject Terms: *PROTEIN structure, *MYCOBACTERIUM tuberculosis, *CELL physiology, *IVERMECTIN, *DRUG development

Structure of the scaffolding protein and portal within the bacteriophage P22 procapsid provides insights into the self-assembly process.

Authors: Xiao, Hao^1,2 (AUTHOR), Chen, Wenyuan¹ (AUTHOR), Pang, Hao^1,3 (AUTHOR), Zheng, Jing¹ (AUTHOR), Wang, Li² (AUTHOR), Feng, Hao² (AUTHOR), Song, Jingdong³ (AUTHOR) songjingdong@ipbcams.ac.cn, Cheng, Lingpeng¹ (AUTHOR) lingpengcheng@hunnu.edu.cn, Liu, Hongrong¹ (AUTHOR) hrliu@hunnu.edu.cn

Source: PLoS Biology. 4/17/2025, Vol. 23 Issue 4, p1-19. 19p.

Subject Terms: *SCAFFOLD proteins, *PROTEIN structure, *BACTERIOPHAGES, *VIRION, *DNA, *HERPESVIRUSES

Toward a Monte Carlo simulation of protein systems in amino-acid sequence space.

Authors: Okamoto, Yuko¹ (AUTHOR) okamoto@cc.nagoya-u.ac.jp

Source: Journal of Chemical Physics. 3/21/2025, Vol. 162 Issue 11, p1-8. 8p.

Subject Terms: *PROTEIN structure, *MONTE Carlo method, *SEQUENCE spaces, *BANKING industry, *AMINO acid sequence

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study.

Authors: Almeida-Juarez AG; Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Chodankar S; National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, United States of America., Pardo-López L; Laboratorio de Biotecnología Marina, Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Zavala-Padilla G; Unidad de Microscopía Electrónica, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Rudiño-Piñera E; Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.

Source: PloS one [PLoS One] 2025 May 05; Vol. 20 (5), pp. e0315992. Date of Electronic Publication: 2025 May 05 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Catechol 1,2-Dioxygenase*/chemistry , Catechol 1,2-Dioxygenase*/metabolism , Bacterial Proteins*/chemistry , Bacterial Proteins*/metabolism, Scattering, Small Angle ; Protein Structure, Quaternary ; Protein Multimerization ; X-Ray Diffraction ; Acinetobacter/enzymology ; Models, Molecular

Chameleon sequences-Structural effects.

Authors: Slupina M; ALSTOM ZWUS Sp. z o.o. Modelarska, Katowice, Poland., Stapor K; Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland., Konieczny L; Chair of Medical Biochemistry, Jagiellonian University - Medical College, Krakow, Poland., Gądek K; Sano Centre for Computational Medicine, Kraków, Poland., Nowakowski P; Sano Centre for Computational Medicine, Kraków, Poland., Roterman I; Department of Bioinformatics and Telemedicine, Jagiellonian University -Medical College, Krakow, Poland.

Source: PloS one [PLoS One] 2025 Apr 22; Vol. 20 (4), pp. e0315901. Date of Electronic Publication: 2025 Apr 22 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry, Hydrophobic and Hydrophilic Interactions ; Protein Structure, Secondary ; Amino Acid Sequence ; Models, Molecular

DeepSS2GO: protein function prediction from secondary structure.

Authors: Song FV; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China., Su J; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China., Huang S; Gemini Data Japan, Kitaku Oujikamiya 1-11-11, 115-0043, Tokyo, Japan., Zhang N; Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, E1 4NS, London, UK., Li K; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China., Ni M; MGI Tech, Beishan Industrial Zone, 518083, Shenzhen, China., Liao M; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China.; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Xueyuan Avenue, 518055, Shenzhen, China.

Source: Briefings in bioinformatics [Brief Bioinform] 2024 Mar 27; Vol. 25 (3).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/metabolism , Proteins*/genetics , Algorithms* , Neural Networks, Computer* , Protein Structure, Secondary* , Computational Biology*/methods, Databases, Protein ; Gene Ontology ; Sequence Analysis, Protein/methods ; Software

Direct coupling analysis and the attention mechanism: Direct Coupling...: F. Caredda, A. Pagnani.

Authors: Caredda, Francesco¹ (AUTHOR) francesco.caredda@polito.it, Pagnani, Andrea^1,2,3 (AUTHOR)

Source: BMC Bioinformatics. 2/6/2025, Vol. 26 Issue 1, p1-21. 21p.

Subject Terms: *PROTEIN structure prediction, *AMINO acid sequence, *LIFE sciences, *TRANSFORMER models, *ENERGY function

Randomly Formed Polyhedral Cages.

Authors: Lukács, Árpád^1,2 (AUTHOR) lukacs.arpad@wigner.hu, Piette, Bernard M. A. G.¹ (AUTHOR) b.m.a.g.piette@durham.ac.uk

Source: Axioms (2075-1680). Feb2025, Vol. 14 Issue 2, p83. 16p.

Subject Terms: *SYNTHETIC proteins, *PROTEIN structure, *POLYHEDRA, *POLYGONS, *GENERALIZATION

Application of copy number variation sequencing combined with whole exome sequencing in prenatal left–right asymmetry disorders.

Authors: Qin, Yu¹ (AUTHOR), Senglong, Muon¹ (AUTHOR), Touch, Koksear¹ (AUTHOR), Xiao, Juan¹ (AUTHOR), Fang, Ruijie¹ (AUTHOR), kang, Qingling¹ (AUTHOR), Fan, Lei¹ (AUTHOR), Li, Shufang¹ (AUTHOR), Liu, Jing¹ (AUTHOR), Wu, Jianli¹ (AUTHOR), Wu, Yuanyuan¹ (AUTHOR), Shi, Xinwei¹ (AUTHOR), Liu, Haiyi¹ (AUTHOR), Gong, Xun¹ (AUTHOR), Lin, Xingguang¹ (AUTHOR), Feng, Ling¹ (AUTHOR), Chen, Suhua¹ (AUTHOR) tj_csh@163.com, Li, Wei¹ (AUTHOR) topliwei@126.com

Source: BMC Genomics. 1/28/2025, Vol. 26 Issue 1, p1-12. 12p.

Subject Terms: *DNA copy number variations, *PROTEIN structure prediction, *SITUS inversus, *GENETIC variation, *LIFE sciences, *FETUS

Association of certain biochemical parameters related to bone cycle with genotype in MPS IIIB patients.

Authors: GÖKKURT, Seda¹, PEKER EYÜBOĞLU, İrem¹ irem.eyuboglu@marmara.edu.tr, NUR GÜZEL, Banu², MIHÇI, Ercan², ÖZER, Ayşe¹, AKKİPRİK, Mustafa¹

Source: Turkish Journal of Medical Sciences. 2025, Vol. 55 Issue 1, p328-336. 9p.

Subject Terms: *MATRIX metalloproteinases, *PROTEIN structure, *NUCLEOTIDE sequencing, *GENETIC mutation, *BONE growth

Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

Authors: Bahai, Akash¹ (AUTHOR), Kwoh, Chee Keong² (AUTHOR), Mu, Yuguang¹ (AUTHOR), Li, Yinghui¹ (AUTHOR) liyh@ntu.edu.sg

Source: PLoS Computational Biology. 12/30/2024, Vol. 20 Issue 12, p1-44. 44p.

Subject Terms: *PROTEIN structure prediction, *TERTIARY structure, *SEQUENCE alignment, *MACHINE learning, *RNA, *DEEP learning

Structural interactions of complex proteins with trehalose: mechanisms for improving the multilevel structure and functional properties of lentil-quinoa protein complexes.

Authors: Alrosan, Mohammad^1,2,3 (AUTHOR) mohammad.alrosan@hotmail.com, Almajwal, Ali Madi⁴ (AUTHOR), Al-Qaisi, Ali⁵ (AUTHOR), Gammoh, Sana⁶ (AUTHOR), Alu'datt, Muhammad H.^6,7 (AUTHOR), Kubow, Stan⁸ (AUTHOR), Tan, Thuan-Chew⁹ (AUTHOR), Bani-Melhem, Khalid¹⁰ (AUTHOR), Razzak Mahmood, Ammar A.¹¹ (AUTHOR)

Source: International Journal of Food Properties. 2024, Vol. 27 Issue 1, p1033-1045. 13p.

Subject Terms: *PROTEIN conformation, *PROTEIN structure, *TREHALOSE, *PROTEIN-protein interactions, *NUTRITIONAL value, *QUINOA

Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction.

Authors: Haque, Neshatul¹ (AUTHOR), Wagenknecht, Jessica B.¹ (AUTHOR), Ratnasinghe, Brian D.¹ (AUTHOR), Zimmermann, Michael T.^1,2,3 (AUTHOR) mtzimmermann@mcw.edu

Source: PLoS ONE. 11/26/2024, Vol. 19 Issue 11, p1-16. 16p.

Subject Terms: *PROTEIN structure prediction, *SYNTHETIC proteins, *SCIENTIFIC knowledge, *PROTEIN conformation, *PROTEIN structure, *DEEP learning

Upstream open reading frames may contain hundreds of novel human exons.

Authors: Ji, Hyun Joo^1,2 (AUTHOR) hji20@jh.edu, Salzberg, Steven L.^1,2,3,4 (AUTHOR) salzberg@jhu.edu

Source: PLoS Computational Biology. 11/20/2024, Vol. 20 Issue 11, p1-14. 14p.

Subject Terms: *PROTEIN structure prediction, *AMINO acid sequence, *PROTEIN structure, *HUMAN genes, *MESSENGER RNA

Structure-aware annotation of leucine-rich repeat domains.

Authors: Xu, Boyan^1,2 (AUTHOR), Cerbu, Alois² (AUTHOR), Tralie, Christopher J.³ (AUTHOR), Lim, Daven⁴ (AUTHOR), Krasileva, Ksenia^1,4 (AUTHOR) kseniak@berkeley.edu

Source: PLoS Computational Biology. 11/5/2024, Vol. 20 Issue 11, p1-17. 17p.

Subject Terms: *PROTEIN structure prediction, *PROTEIN structure, *AMINO acid sequence, *PROTEIN models, *PROTEIN domains, *DEEP learning