Ahmad S - Search Results

1

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.

2

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.

3

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.

4

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.

5

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.

6

Inadequacy of Evolutionary Profiles Vis-a-vis Single Sequences in Predicting Transient DNA-Binding Sites in Proteins.

Arya A, Mary Varghese D, Kumar Verma A, Ahmad S. Arya A, et al. Among authors: ahmad s. J Mol Biol. 2022 Jul 15;434(13):167640. doi: 10.1016/j.jmb.2022.167640. Epub 2022 May 18. J Mol Biol. 2022. PMID: 35597551

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

Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence.

Chauhan S, Ahmad S. Chauhan S, et al. Among authors: ahmad s. Proteins. 2020 Jan;88(1):15-30. doi: 10.1002/prot.25763. Epub 2019 Jul 8. Proteins. 2020. PMID: 31228283

9

ECG anomaly class identification using LSTM and error profile modeling.

Chauhan S, Vig L, Ahmad S. Chauhan S, et al. Among authors: ahmad s. Comput Biol Med. 2019 Jun;109:14-21. doi: 10.1016/j.compbiomed.2019.04.009. Epub 2019 Apr 16. Comput Biol Med. 2019. PMID: 31030180

10

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins.

Nagarajan R, Ahmad S, Gromiha MM. Nagarajan R, et al. Among authors: ahmad s. Nucleic Acids Res. 2013 Sep;41(16):7606-14. doi: 10.1093/nar/gkt544. Epub 2013 Jun 20. Nucleic Acids Res. 2013. PMID: 23788679 Free PMC article.

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