Ahmad S - Search Results

1

Host-pathogen protein-nucleic acid interactions: A comprehensive review.

Jain A, Mittal S, Tripathi LP, Nussinov R, Ahmad S. Jain A, et al. Among authors: ahmad s. Comput Struct Biotechnol J. 2022 Aug 4;20:4415-4436. doi: 10.1016/j.csbj.2022.08.001. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 36051878 Free PMC article. Review.

2

Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.

Ahmad S, Keskin O, Sarai A, Nussinov R. Ahmad S, et al. Nucleic Acids Res. 2008 Oct;36(18):5922-32. doi: 10.1093/nar/gkn573. Epub 2008 Sep 18. Nucleic Acids Res. 2008. PMID: 18801847 Free PMC article.

3

CCRXP: exploring clusters of conserved residues in protein structures.

Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R. Ahmad S, et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401. doi: 10.1093/nar/gkq360. Epub 2010 May 10. Nucleic Acids Res. 2010. PMID: 20457748 Free PMC article.

4

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter.

Tiwari P, Tripathi LP, Nishikawa-Matsumura T, Ahmad S, Song SN, Isobe T, Mizuguchi K, Yoshizaki K. Tiwari P, et al. Among authors: ahmad s. Biochim Biophys Acta. 2013 Jun;1830(6):3650-5. doi: 10.1016/j.bbagen.2013.01.024. Epub 2013 Feb 5. Biochim Biophys Acta. 2013. PMID: 23391827

5

Integrated pathway clusters with coherent biological themes for target prioritisation.

Chen YA, Tripathi LP, Dessailly BH, Nyström-Persson J, Ahmad S, Mizuguchi K. Chen YA, et al. Among authors: ahmad s. PLoS One. 2014 Jun 11;9(6):e99030. doi: 10.1371/journal.pone.0099030. eCollection 2014. PLoS One. 2014. PMID: 24918583 Free PMC article.

6

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S. Andrabi M, et al. Among authors: ahmad s. Sci Rep. 2017 Jun 22;7(1):4071. doi: 10.1038/s41598-017-03199-6. Sci Rep. 2017. PMID: 28642456 Free PMC article.

7

Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.

Ahmad S, Prathipati P, Tripathi LP, Chen YA, Arya A, Murakami Y, Mizuguchi K. Ahmad S, et al. Nucleic Acids Res. 2018 Jan 9;46(1):54-70. doi: 10.1093/nar/gkx1166. Nucleic Acids Res. 2018. PMID: 29186632 Free PMC article.

8

Unraveling molecular mechanisms of head and neck cancer.

Antra, Parashar P, Hungyo H, Jain A, Ahmad S, Tandon V. Antra, et al. Among authors: ahmad s. Crit Rev Oncol Hematol. 2022 Oct;178:103778. doi: 10.1016/j.critrevonc.2022.103778. Epub 2022 Aug 4. Crit Rev Oncol Hematol. 2022. PMID: 35932993 Review.

9

Predictive modeling of moonlighting DNA-binding proteins.

Varghese DM, Nussinov R, Ahmad S. Varghese DM, et al. Among authors: ahmad s. NAR Genom Bioinform. 2022 Dec 2;4(4):lqac091. doi: 10.1093/nargab/lqac091. eCollection 2022 Dec. NAR Genom Bioinform. 2022. PMID: 36474806 Free PMC article.

10

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks.

Andrabi M, Mizuguchi K, Sarai A, Ahmad S. Andrabi M, et al. Among authors: ahmad s. BMC Struct Biol. 2009 May 13;9:30. doi: 10.1186/1472-6807-9-30. BMC Struct Biol. 2009. PMID: 19439068 Free PMC article.

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