Computational Biology @ IITGN

Publications

  1. Shashank Kumar Singh, Ashutosh Srivastava (2024); Decoding the plant clock: a review of mathematical models for the circadian regulatory network. Plant Mol Biol , 114, 93 (2024). https://doi.org/10.1007/s11103-024-01493-2
  2. Shriyansh Srivastava, Rakesh Thakur, and Ashutosh Srivastava (2024); Investigating REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators. BioRxiv, 2024.04.13.589008. https://doi.org/10.1101/2024.04.13.589008
  3. Dhara, Palash, Niyati Shah, Vidya Sundaram, Ashutosh Srivastava, Alexander A. Solovev, Yongfeng Mei, Dmitry A. Gorin, and Krishna Kanti Dey (2024); Influence of Protein Nativity on the Stability of Bovine Serum Albumin Coated Microbubbles. iScience, 109286.
  4. Sayantoni Chaudhuri and Ashutosh Srivastava (2022); Network approach to understand biological systems: From single to multilayer networks. Journal of Biosciences, 47, 4, 1-18
  5. Albert M Schulte, Dušan Kolarski, Vidya Sundaram, Ashutosh Srivastava, Florence Tama, Ben L Feringa, Wiktor Szymanski (2022); Light-Control over Casein Kinase 1δ Activity with Photopharmacology: A Clear Case for Arylazopyrazole-Based Inhibitors. International Journal of Molecular Sciences, 23, 10, 5326
  6. RP Vivek-Ananth, Ajaya Kumar Sahoo, Ashutosh Srivastava*, Areejit Samal* (2022); Virtual screening of phytochemicals from Indian medicinal plants against the endonuclease domain of SFTS virus L polymerase. RSC Advances, 12, 10, 6234-6247
  7. Simon Miller#, Ashutosh Srivastava#, Yoshiko Nagai, Yoshiki Aikawa, Florence Tama, and Tsuyoshi Hirota (2021); Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation. PNAS, 118, 26, e2026191118 (#Equal Contribution)
  8. Dušan Kolarski, Carla Miró Vinyals, Akiko Sugiyama, Kenichiro Itami, Ashutosh Srivastava, Florence Tama, Wiktor Szymanski, Tsuyoshi Hirota, Ben L. Feringa (2021), Reversible Modulation of Circadian Time with Chronophotopharmacology, Nature Communications, 12, 3164.
  9. Dusan. Kolarski, Simon Miller, Tsuyoshi. Oshima, Yoshiko. Nagai, Yugo. Aoki, Piermichele Kobauri, Ashutosh Srivastava et al., (2021), Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock, Journal of the American Chemical Society, 143, 4, 2078–2087.
  10. Ashutosh Srivastava*, Varun Birari, Somdatta Sinha*, (2020) Small conformational changes underlie evolution of resistance to NNRTI in HIV Reverse Transcriptase, Biophysical Journal, 118, 2489-2501. (*Corresponding Author)
  11. Simon Miller, You Lee Son, Yoshiki Aikawa, Eri Makino, Yoshiko Nagai, Ashutosh Srivastava, et al. (2020); Isoform-selective regulation of mammalian cryptochromes. Nature Chemical Biology, 16, 676-685.
  12. Jennifer Fribourgh#, Ashutosh Srivastava#, Colby Sandate# et al. (2020); Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing; eLife; 9:e55275 (#Equal Contribution)
  13. Ashutosh Srivastava, Sandhya P. Tiwari, Osamu Miyashita and Florence Tama (2020); Integrative/Hybrid modeling approaches for studying biomolecules, Journal of Molecular Biology, 432, 2846-2860.
  14. Aarthi Putarjunan, Jim Ruble, Ashutosh Srivastava, et al. (2019); Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP Kinases to SPEECHLESS, Nature Plants,5,  742–754.
  15. Tsuyoshi Oshima, Yoshimi Niwa, Keiko Kuwata, Ashutosh Srivastava, et al.(2019); Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth; Science Advances, 5, 1, eaau9060
  16. Ashutosh Srivastava, Tetsuro Nagai, Arpita Srivastava, Osamu Miyashita, Florence Tama (2018); Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics, International Journal of Molecular Sciences, 19(11):3401.
  17. Ashutosh Srivastava, Tsuyoshi Hirota, Stephan Irle, Florence Tama (2018); Conformational dynamics of human Protein Kinase CK2α and its effect on function and inhibition. Proteins, 86, 344–353.
  18. Ashutosh Srivastava, Somdatta Sinha (2017); Uncoupling of ammonia channel as a mechanism of allosteric inhibition in Anthranilate Synthase of Serratia marcescens: dynamic and graph theoretic analysis. Molecular BioSystems, 13, 142-155.
  19. Ashutosh Srivastava, Somdatta Sinha (2014); Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective. PLoS ONE 9(8): e102856.