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M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures.

• Authors : Sheikholeslami M; Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib, Isfahan, 817416 - 73461, Iran. .; Nazari MH

Subjects: Molecular Docking Simulation*/Molecular Docking Simulation*/Molecular Docking Simulation*/methods ; Peptides*/Peptides*/Peptides*/chemistry ; Proteins*/Proteins*/Proteins*/chemistry

• Source: BMC bioinformatics [BMC Bioinformatics] 2025 Apr 14; Vol. 26 (1), pp. 102. Date of Electronic Publication: 2025 Apr Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105

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Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein

• Authors : Reji Manjunathan; Vijayalakshmi Periyaswami; Kartik Mitra

Subjects: Transmembrane serine protease 2; SARS-Cov-2 coronavirus; Phyto compounds

• Source: BMC Bioinformatics, Vol 23, Iss 1, Pp 1-15 (2022)

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A comprehensive survey of scoring functions for protein docking models.

• Authors : Shirali, Azam¹ (AUTHOR) ; Stebliankin, Vitalii¹ (AUTHOR) ; Karki, Ukesh² (AUTHOR)

• Source: BMC Bioinformatics. 1/22/2025, Vol. 26 Issue 1, p1-25. 25p.

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Benchmarking of different molecular docking methods for protein-peptide docking.

• Authors : Agrawal, Piyush^1,2 ; Singh, Harinder² ; Srivastava, Hemant Kumar²

• Source: BMC Bioinformatics. 2/4/2019 Supplement 13, Vol. 19 Issue 13, p105-124. 20p. 1 Diagram, 12 Charts, 3 Graphs.

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Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes.

• Authors : Shen, Jie¹; Wenqian Zhang¹; Hong Fang²

• Source: BMC Bioinformatics. 2013, Vol. 14 Issue Suppl 14, p1-11. 11p. 5 Diagrams, 1 Chart, 2 Graphs.

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CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins.

• Authors : Park, Ho-min^1,2 (AUTHOR); Won, Jongbum¹ (AUTHOR); Park, Yunseol¹ (AUTHOR)

• Source: BMC Bioinformatics. 4/25/2023, Vol. 24 Issue 1, p1-6. 6p.

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Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists

• Authors : Wenqian Zhang; Weigong Ge; Roger Perkins

Subjects: 0301 basic medicine; Estrogen Receptor alpha; Estrogens

• Source: BMC Bioinformatics

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Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development.

• Authors : Su CT; Bioinformatics Research Centre, School of Computer Engineering, Nanyang Technological University, Singapore.; Schönbach C

Subjects: Influenza A Virus, H1N1 Subtype* ; Influenza A Virus, H5N1 Subtype* ; Molecular Docking Simulation*

• Source: BMC bioinformatics [BMC Bioinformatics] 2013; Vol. 14 Suppl 2, pp. S21. Date of Electronic Publication: 2013 Jan 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Parallel multi-swarm cooperative particle swarm optimization for protein–ligand docking and virtual screening.

• Authors : Li, Chao¹ (AUTHOR); Li, Jinxing¹ (AUTHOR); Sun, Jun¹ (AUTHOR)

• Source: BMC Bioinformatics. 5/30/2022, Vol. 23 Issue 1, p1-17. 17p.

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TRain: T-cell receptor automated immunoinformatics.

• Authors : Seamann A; School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska at Omaha, 1110 S 67TH, Omaha, NE, 68182, USA.; Bennett-Boehm M

Subjects: Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/chemistry ; Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/metabolism ; Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/Receptors, Antigen, T-Cell*/immunology

• Source: BMC bioinformatics [BMC Bioinformatics] 2025 Mar 06; Vol. 26 (1), pp. 76. Date of Electronic Publication: 2025 Mar 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105

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