Adam, K., Gyorgypal, Z., & Hegedus, Z. (2020). DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments. Bioinformatics, 36(7), 2286–2287.
Agarwal, S., & Cho, T. Y. (2018). Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter. Nucleic Acids Research, 46(2), 929–941.
Alves, C. C., Donadi, E. A., & Giuliatti, S. (2021). Structural characterization of the interaction of hypoxia inducible factor-1 with its hypoxia responsive element at the- 964g> a variation site of the hla-g promoter region. International Journal of Molecular Sciences, 22(23), 13046.
Aragón, E., Wang, Q., Zou, Y., Morgani, S. M., Ruiz, L., Kaczmarska, Z., Su, J., Torner, C., Tian, L., Hu, J., & others. (2019). Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling. Genes & Development, 33(21–22), 1506–1524.
Bax, A. (2023). How acidic amino acid residues facilitate DNA target site selection.
Bera, S., Shi, K., Aihara, H., Grandgenett, D. P., & Pandey, K. K. (2023). Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. Journal of Biological Chemistry, 299(6).
Berman, H. M., Lawson, C. L., & Schneider, B. (2022). Developing community resources for nucleic acid structures. Life, 12(4), 540.
Bersten, D., Sullivan, A., McDougal, D., Breen, J., Fitzsimmons, R., Muscat, G., Pederson, S., Bruning, J., Fan, C., Thomas, P., & others. (2022). Core and Flanking bHLH-PAS: DNA interactions mediate specificity and drive obesity. BioRxiv, 2022–02.
Bhakta, S., & Saha, A. (2020). An investigation to study the effects of cyclic-AMP to cAMP receptor protein from Mycobacterium tuberculosis by computational approach. Journal of Physics: Conference Series, 1579(1), 012025.
Chen, J., Qi, Y., Duan, Y., Duan, M., & Yang, M. (2020). C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal. Proteins: Structure, Function, and Bioinformatics, 88(11), 1401–1412.
Chen, Q., Chuai, G., Zhang, H., Tang, J., Duan, L., Guan, H., Li, W., Li, W., Wen, J., Zuo, E., & others. (2023). Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints. Nature Communications, 14(1), 7521.
Chen, Y., Liu, H., Yang, C., Gao, Y., Yu, X., Chen, X., Cui, R., Zheng, L., Li, S., Li, X., & others. (2019). Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Nature Communications, 10(1), 387.
Chiu, T.-P. (2018). Genome-Wide Studies of Protein-DNA Binding: Beyond Sequence towards Biophysical and Physicochemical Models [Phdthesis]. University of Southern California.
Chiu, T.-P., Rao, S., Mann, R. S., Honig, B., & Rohs, R. (2017). Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding. Nucleic Acids Research, 45(21), 12565–12576.
Chiu, T.-P., Rao, S., & Rohs, R. (2023). Physicochemical models of protein–DNA binding with standard and modified base pairs. Proceedings of the National Academy of Sciences, 120(4), e2205796120.
Ciges-Tomas, J. R., Alite, C., Humphrey, S., Donderis, J., Bowring, J., Salvatella, X., Penadés, J. R., & Marina, A. (2019). The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Nature Communications, 10(1), 3676.
Comoglio, F., Simonatto, M., Polletti, S., Liu, X., Smale, S. T., Barozzi, I., & Natoli, G. (2019). Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. Genes & Development, 33(17–18), 1159–1174.
Corona, R. I., Sudarshan, S., Aluru, S., & Guo, J. (2018). An SVM-based method for assessment of transcription factor-DNA complex models. BMC Bioinformatics, 19, 49–57.
Cui, F., Zhang, Z., Cao, C., Zou, Q., Chen, D., & Su, X. (2022). Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data. Proteomics, 22(8), 2100197.
Dantas Machado, A. C., Cooper, B. H., Lei, X., Di Felice, R., Chen, L., & Rohs, R. (2020). Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. Nucleic Acids Research, 48(15), 8529–8544.
Dapkūnas, J., Timinskas, A., Olechnovič, K., Tomkuvienė, M., & Venclovas, Č. (2024). PPI3D: a web server for searching, analyzing and modeling protein–protein, protein–peptide and protein–nucleic acid interactions. Nucleic Acids Research, gkae278.
Dey, U., Sarkar, S., Teronpi, V., Yella, V. R., & Kumar, A. (2021). G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation. Biochimie, 184, 40–51.
Duckworth, A. T., Ducos, P. L., McMillan, S. D., Satyshur, K. A., Blumenthal, K. H., Deorio, H. R., Larson, J. A., Sandler, S. J., Grant, T., & Keck, J. L. (2023). Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli. Nature Communications, 14(1), 2725.
Gallego, D., Darre, L., Dans, P. D., & Orozco, M. (2019). VeriNA3d: an R package for nucleic acids data mining. Bioinformatics, 35(24), 5334–5336.
Ghadirian, N. (2022). DNA Binding Protein’s Structure, Mechanism, and Functional Relevance; from Filament Formation of SgrAI to Helicase Activity of B19V-NS1 [Phdthesis]. The University of Arizona.
Gharouni, M., Mosaddeghi, H., Mehrzad, J., Es-Haghi, A., & Motavalizadehkakhky, A. (2021). In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach. Journal of Molecular Modeling, 27(2), 40.
Hartley, S. (2020). DNA Damage Recognition and UvrB Loading by UvrA within the Nucleotide Excision Repair Pathway [Phdthesis]. City University of New York.
Hashmi, H. F., Waseem, M., Ali, S. S., Hussain, Z., & Chen, K. (2021). Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein–Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis. Frontiers in Molecular Biosciences, 8, 664436.
Holden, J. K., & Cunningham, C. N. (2018). Targeting the hippo pathway and cancer through the TEAD family of transcription factors. Cancers, 10(3), 81.
Hossain, K. A. (2023). Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms.
Hossain, K. A., Kogut, M., Słabońska, J., Sappati, S., Wieczór, M., & Czub, J. (2023). How acidic amino acid residues facilitate DNA target site selection. Proceedings of the National Academy of Sciences, 120(3), e2212501120.
Huber, E. M., Hortschansky, P., Scheven, M. T., Misslinger, M., Haas, H., Brakhage, A. A., & Groll, M. (2021). Cooperative DNA base and shape recognition by the CCAAT-binding complex and its bZIP transcription factor HapX. BioRxiv, 2021–07.
Huber, E. M., Hortschansky, P., Scheven, M. T., Misslinger, M., Haas, H., Brakhage, A. A., & Groll, M. (2022). Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX. Structure, 30(7), 934–946.
Huesa, J., Giner-Lamia, J., Pucciarelli, M. G., Paredes-Martı́nez, F., Portillo, F. G., Marina, A., & Casino, P. (2021). Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon. Nucleic Acids Research, 49(4), 2357–2374.
Jain, P., & Sudandiradoss, C. (2023). Andrographolide-based potential anti-inflammatory transcription inhibitors against nuclear factor NF-kappa-B p50 subunit (NF-κB p50): an integrated molecular and quantum mechanical approach. 3 Biotech, 13(1), 15.
Jha, A., Saha, S., Ayasolla, K., Vashistha, H., Malhotra, A., Skorecki, K., & Singhal, P. C. (2020). MiR193a modulation and podocyte phenotype. Cells, 9(4), 1004.
Jones, M., Khanna, S., & Ferguson, A. (n.d.). FlowBack: A Flow-matching Approach for Generative Backmapping of Macromolecules. ICML’24 Workshop ML for Life and Material Science: From Theory to Industry Applications.
Jones, M. S., Shmilovich, K., & Ferguson, A. L. (2023). DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces. Journal of Chemical Theory and Computation, 19(21), 7908–7923.
Jóźwik, I. K., Li, W., Zhang, D.-W., Wong, D., Grawenhoff, J., Ballandras-Colas, A., Aiyer, S., Cherepanov, P., Engelman, A. N., & Lyumkis, D. (2022). B-to-A transition in target DNA during retroviral integration. Nucleic Acids Research, 50(15), 8898–8918.
Kabir, M. W. U., Alawad, D., Shah, K., Howladar, N., Farooq, M., Benkara, S., Rajbhandari, A., Pham, D., Pierre, J., & Hoque, M. T. (n.d.). AI-based Integrated Approach for Gene Protein Regulatory Network.
KAMAL, H., ZAFAR, M. M., RAZZAQ, A., IJAZ, A., ANVAR, Z., TOPÇU, H., ELHINDI, K. M., SAEED, A., FATIMA, U., & JIANG, X. (2024). Using computational modeling to design antiviral strategies and understand plant-virus interactions. Turkish Journal of Agriculture and Forestry, 48(3), 417–429.
Kang, K., Wang, L., & Song, C. (2023). ProtRAP: Predicting lipid accessibility together with solvent accessibility of proteins in one run. Journal of Chemical Information and Modeling, 63(3), 1058–1065.
Karn, R., & Emerson, I. A. (2020). Breast cancer mutation in GATA3 zinc finger 1 induces conformational changes leading to the closer binding of ZnFn2 with a wrapping architecture. Journal of Biomolecular Structure and Dynamics.
Kaur, S., Sisodia, R., Gupta, B., Madhurantakam, C., & Singh, A. (2023). Combinatorial interactions among natural structural variants of Brassica SOC1 promoters and SVP depict conservation of binding affinity despite molecular diversity.
Kavita, P. (n.d.). Computational resources, Biological databases and tools of biological analysis.
Kennedy, Madison A, Hosford, C. J., Azumaya, C. M., Luyten, Y. A., Chen, M., Morgan, R. D., & Stoddard, B. L. (2023). Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI. Nucleic Acids Research, 51(9), 4467–4487.
Kennedy, Madison Arza. (2023). Structural and Mechanistic Studies of the Type IIS Restriction Endonuclease PaqCI and De Novo Designed Circular Tandem Repeat Proteins [Phdthesis]. University of Washington.
Khan, A., Khan, M. T., Saleem, S., Junaid, M., Ali, A., Ali, S. S., Khan, M., & Wei, D.-Q. (2020). Structural insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein. Computational and Structural Biotechnology Journal, 18, 2174–2184.
Khatoon, H., Raza, R. Z., Saleem, S., Batool, F., Arshad, S., Abrar, M., Ali, S., Hussain, I., Shubin, N. H., & Abbasi, A. A. (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Molecular and Cell Biology, 24(1), 13.
Kribelbauer, J. F., Lu, X.-J., Rohs, R., Mann, R. S., & Bussemaker, H. J. (2020). Toward a mechanistic understanding of DNA methylation readout by transcription factors. Journal of Molecular Biology, 432(6), 1801–1815.
Lambert, S. A., Yang, A. W., Sasse, A., Cowley, G., Albu, M., Caddick, M. X., Morris, Q. D., Weirauch, M. T., & Hughes, T. R. (2019). Similarity regression predicts evolution of transcription factor sequence specificity. Nature Genetics, 51(6), 981–989.
Lara-Gonzalez, S., Dantas Machado, A. C., Rao, S., Napoli, A. A., Birktoft, J., Di Felice, R., Rohs, R., & Lawson, C. L. (2020). The RNA polymerase α subunit recognizes the DNA shape of the upstream promoter element. Biochemistry, 59(48), 4523–4532.
Lawson, C. L., Berman, H. M., Chen, L., Vallat, B., & Zirbel, C. L. (2024). The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids. Nucleic Acids Research, 52(D1), D245–D254.
Lei, X., Zhao, J., Sagendorf, J. M., Rajashekar, N., Xu, J., Machado, A. C. D., Sen, C., Rohs, R., Feng, P., & Chen, L. (2020). Crystal Structures of Ternary Complexes of MEF2 and NKX2–5 Bound to DNA Reveal a Disease Related Protein–Protein Interaction Interface. Journal of Molecular Biology, 432(19), 5499–5508.
Li, J., Dantas Machado, A. C., Guo, M., Sagendorf, J. M., Zhou, Z., Jiang, L., Chen, X., Wu, D., Qu, L., Chen, Z., & others. (2017). Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site. Biochemistry, 56(29), 3745–3753.
Lin, M. (2020). Toward Understanding Protein-DNA Interactions [Phdthesis]. The University of North Carolina at Charlotte.
Lin, M., Malik, F. K., & Guo, J. (2021). A comparative study of protein–ssDNA interactions. NAR Genomics and Bioinformatics, 3(1), lqab006.
Liu, X., Weikum, E. R., Tilo, D., Vinson, C., & Ortlund, E. A. (2021). Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. Nucleic Acids Research, 49(15), 8923–8933.
Lountos, G. T., Cherry, S., Tropea, J. E., Wlodawer, A., & Miller, M. (2022). Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter. Journal of Structural Biology, 214(4), 107918.
Lu, X.-J. (n.d.). An Overview (User Manual for DSSR 2.3).
Lu, X.-J. (2020). DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Nucleic Acids Research, 48(13), e74–e74.
Luyten, Y. A., Hausman, D. E., Young, J. C., Doyle, L. A., Higashi, K. M., Ubilla-Rodriguez, N. C., Lambert, A. R., Arroyo, C. S., Forsberg, K. J., Morgan, R. D., & others. (2022). Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Research, 50(9), 5171–5190.
Malbranke, C., Rostain, W., Depardieu, F., Cocco, S., Monasson, R., & Bikard, D. (2023). Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment. PLOS Computational Biology, 19(11), e1011621.
Malik, A., Jayarathna, D. K., Fisher, M., Barbhuiya, T. K., Gandhi, N. S., & Batra, J. (2024). Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4. Proteins: Structure, Function, and Bioinformatics, 92(2), 282–301.
Mallona, I., Ilie, I. M., Karemaker, I. D., Butz, S., Manzo, M., Caflisch, A., & Baubec, T. (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1), 145–157.
Marcos-Torres, F. J., Maurer, D., Juniar, L., & Griese, J. J. (2021). The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout. Nucleic Acids Research, 49(17), 10120–10135.
Miller, I., Totrov, M., Korotchkina, L., Kazyulkin, D. N., Gudkov, A. V., & Korolev, S. (2021). Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Research, 49(19), 11350–11366.
Moniot, A., Guermeur, Y., de Vries, S. J., & Chauvot de Beauchene, I. (2022). ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. Bioinformatics, 38(16), 3911–3917.
Mukherjee, S., & Nithin, C. (2022). Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces. In Advances in Protein Molecular and Structural Biology Methods (pp. 163–180). Elsevier.
Mumtaz, K., Hussain, I., Iftikhar, F., Rehman, F. U., Jameel, M., Farooq, S., Hassan, H., Fatima, A., Ottmann, O. G., & Mian, A. A. (2023). Prioritization of The Zinc finger domain within BCL11A by the Amelioration capability of hemoglobinopathies using CRISPR-Cas9 technology. BioRxiv, 2023–11.
Nematzadeh, S., Aydin, N., Kurt, Z., & Torkamanian-Afshar, M. (2024). NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins. Current Bioinformatics, 19(4), 385–397.
Ocampo Mahecha, S. J. (n.d.). Caracterización funcional de variantes (SNV, Indels, CNVs) analizadas por medios computacionales en 5 familias dominicanas con labio y/o paladar hendido no sindrómico [Phdthesis]. Universidad Nacional de Colombia.
Pal, A., Chakrabarti, P., & Dey, S. (2022). ProDFace: A web-tool for the dissection of protein-DNA interfaces. Frontiers in Molecular Biosciences, 9, 978310.
Park, J., Herrmann, G. K., Mitchell, P. G., Sherman, M. B., & Yin, Y. W. (2023). Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity. Nature Structural & Molecular Biology, 30(6), 812–823.
Poddar, S., Chakravarty, D., & Chakrabarti, P. (2018). Structural changes in DNA-binding proteins on complexation. Nucleic Acids Research, 46(7), 3298–3308.
Pradhan, S. (2023). Computational insights into the central role of Xeroderma pigmentosum group A (XPA) protein in nucleotide excision repair (NER) [Phdthesis]. Tezpur University.
Pradhan, S., & Mattaparthi, V. S. K. (2018). Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA98–210) with damaged DNA. Journal of Biomolecular Structure and Dynamics, 36(13), 3341–3353.
Ranjan, P., Yadav, A., Behera, A. K., Singh, D. K., Singh, P., & Singh, G. P. (2024). Structural, functional and evolutionary analysis of wheat WRKY45 protein: A combined bioinformatics and MD simulation approach. Cereal Research Communications, 52(2), 489–499.
Ray, A., & Di Felice, R. (2020). Protein-mutation-induced conformational changes of the DNA and nuclease domain in CRISPR/Cas9 systems by molecular dynamics simulations. The Journal of Physical Chemistry B, 124(11), 2168–2179.
Ray, S., Tillo, D., Assad, N., Ufot, A., Deppmann, C., Durell, S. R., Porollo, A., & Vinson, C. (2018). Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA. Biochemical and Biophysical Research Communications, 501(4), 905–912.
Ribeiro, J., Rı́os-Vera, C., Melo, F., & Schüller, A. (2019). Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions. Bioinformatics, 35(18), 3499–3501.
Rogers, J. M., Waters, C. T., Seegar, T. C., Jarrett, S. M., Hallworth, A. N., Blacklow, S. C., & Bulyk, M. L. (2019). Bispecific forkhead transcription factor FoxN3 recognizes two distinct motifs with different DNA shapes. Molecular Cell, 74(2), 245–253.
Roy, T. B., & Sarma, S. P. (2023). Insights into the solution structure and transcriptional regulation of the MazE9 antitoxin in Mycobacterium tuberculosis. Proteins: Structure, Function, and Bioinformatics.
Sagendorf, J. M., Markarian, N., Berman, H. M., & Rohs, R. (2020). DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes. Nucleic Acids Research, 48(D1), D277–D287.
Santiago-Frangos, A., Henriques, W. S., Wiegand, T., Gauvin, C. C., Buyukyoruk, M., Graham, A. B., Wilkinson, R. A., Triem, L., Neselu, K., Eng, E. T., & others. (2023). Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Nature Structural & Molecular Biology, 30(11), 1675–1685.
Santiago-Frangos, A., Henriques, W., Wiegand, T., Gauvin, C., Buyukyoruk, M., Neselu, K., Eng, E., Lander, G., Wilkinson, R., Graham, A., & others. (2023). Protein-mediated folding of the genome is essential for site-specific integration of foreign DNA into CRISPR loci.
Saragi, R. T., & others. (2022). Non-covalent interactions in thiol aggregates and nucleoside-amino acid binding models.
Schmidt, J. M., & Bleichert, F. (2020). Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nature Communications, 11(1), 4263.
Schnepf, M., von Reutern, M., Ludwig, C., Jung, C., & Gaul, U. (2020). Transcription factor binding affinities and DNA shape readout. Iscience, 23(11).
Seifert-Davila, W., Chaban, A., Baudin, F., Girbig, M., Hauptmann, L., Hoffmann, T., Duss, O., Eustermann, S., & Muller, C. W. (2024). Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC. BioRxiv, 2024–08.
Shan, Z., Ghadirian, N., Lyumkis, D., & Horton, N. C. (2022). Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity. Journal of Biological Chemistry, 298(4).
Sharma, N., Thompson, M. K., Arrington, J. F., Terry, D. M., Chakravarthy, S., Prevelige, P. E., & Prakash, A. (2022). Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A. Frontiers in Cell and Developmental Biology, 10, 893806.
Shi, H. (2021). Resolving Atomic-resolution Nucleic Acid Ensembles Using Solution State Nuclear Magnetic Resonance [Phdthesis]. Duke University.
Shi, H., Kimsey, I. J., Gu, S., Liu, H.-F., Pham, U., Schumacher, M. A., & Al-Hashimi, H. M. (2021). Revealing AT and GC Hoogsteen base pairs in stressed protein-bound duplex DNA. Nucleic Acids Research, 49(21), 12540–12555.
Silva, C. S., Nayak, A., Lai, X., Hutin, S., Hugouvieux, V., Jung, J.-H., López-Vidriero, I., Franco-Zorrilla, J. M., Panigrahi, K. C., Nanao, M. H., & others. (2020). Molecular mechanisms of Evening Complex activity in Arabidopsis. Proceedings of the National Academy of Sciences, 117(12), 6901–6909.
Smiley, Adam T, Tompkins, K. J., Pawlak, M. R., Krueger, A. J., Evans III, R. L., Shi, K., Aihara, H., & Gordon, W. R. (2023). Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. Mbio, 14(1), e02587-22.
Smiley, Adam Trey. (2024). From Basic Science to Biotechnology: Characterizing and Developing HUH-Endonucleases for Diverse Applications [Phdthesis]. University of Minnesota.
Srivastava, D., Gowribidanur-Chinnaswamy, P., Gaur, P., Spies, M., Swaroop, A., & Artemyev, N. O. (2024). Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element. Structure.
Tanshee, R. R., Mahmud, Z., Nabi, A. N., & Sayem, M. (2024). A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences. Plos One, 19(9), e0309713.
TICHÁ, A. (n.d.). bázovỳch pár\uu v DNA a DNA/protein komplexech.
Tillo, D., Ray, S., Syed, K.-S., Gaylor, M. R., He, X., Wang, J., Assad, N., Durell, S. R., Porollo, A., Weirauch, M. T., & others. (2017). The Epstein-Barr virus B-ZIP protein Zta recognizes specific DNA sequences containing 5-methylcytosine and 5-hydroxymethylcytosine. Biochemistry, 56(47), 6200–6210.
Tompkins, Kassidy J, Houtti, M., Litzau, L. A., Aird, E. J., Everett, B. A., Nelson, A. T., Pornschloegl, L., Limón-Swanson, L. K., Evans III, R. L., Evans, K., & others. (2021). Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Research, 49(2), 1046–1064.
Tompkins, Kassidy James. (2021). HUH-endonuclease Mediated Protein-DNA Bioconjugation [Phdthesis]. University of Minnesota.
Ullah, S., Rahman, W., Ullah, F., Ullah, A., Ahmad, G., Ijaz, M., Ullah, H., & Sharafmal, D. M. (2024). The HABD: Home of All Biological Databases Empowering Biological Research With Cutting-Edge Database Systems. Current Protocols, 4(5), e1063.
Vakser, I. A., & Deeds, E. J. (2019). Computational approaches to macromolecular interactions in the cell. Current Opinion in Structural Biology, 55, 59–65.
Wan, T., Horová, M., Beltran, D. G., Li, S., Wong, H.-X., & Zhang, L.-M. (2021). Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Molecular Cell, 81(14), 2887–2900.
Weissmann, F., Greiwe, J. F., Pühringer, T., Miller, T. C., Diffley, J. F., & Costa, A. (2024). MCM Double Hexamer Loading Visualised with Human Proteins. BioRxiv, 2024–04.
Wu, Y., Xie, L., Jiang, Y., & Li, T. (2022). Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: a review. International Journal of Biological Macromolecules, 206, 188–202.
Yang, O., Choi, S., Seo, D., Choi, S., Kim, Y., Lee, C., Lee, E., Baek, J., Kim, K., & Lee, H. (2020). Implementing a Web-based Seed Phenotype Trait Visualization Support System. Journal of the Korea Industrial Information Systems Research, 25(5), 83–90.
Yang, X., Wang, Y., Liu, G., Deng, Z., Lin, S., & Zheng, J. (2022). Structural basis of Streptomyces transcription activation by zinc uptake regulator. Nucleic Acids Research, 50(14), 8363–8376.
Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2024). Interpretable Protein-DNA Interactions Captured by Structure-based Optimization. BioRxiv, 2024–05.
Zhu, F., Farnung, L., Kaasinen, E., Sahu, B., Yin, Y., Wei, B., Dodonova, S. O., Nitta, K. R., Morgunova, E., Taipale, M., & others. (2018). The interaction landscape between transcription factors and the nucleosome. Nature, 562(7725), 76–81.
Zia, A., & Rashid, S. (2021). Systematic transition modeling analysis in the MEF2B-DNA binding interface due to Y69H and K4E variants. Journal of Molecular Graphics and Modelling, 108, 108009.