PI Publications
- 2024In silico and structure-based evaluation of deleterious mutations identified in human Chk1, Chk2, and Wee1 protein kinase. Journal of Cellular Biochemistry. 125(1):89-99.
Colaco V, Goswami N, Goel VK, Srivastava SK, Lalrohlua P, Senthil Kumar N, Borah P, Baruah R, Varma AK (2024)
Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1. Proteins. 92(4):540-553.Mishra N, Dubey S, Kumari A, Khan MA, Kuligina ES, Preobrazhenskaya EV, Romanko AA, Yadav LR, Sarin R, Imyanitov EN, Varma AK (2024).
Structural dynamics of clinically-reported VUS in the BARD1 ARD-BRCT region to predict the molecular basis of alterations. Journal of Biomolecular Structure and Dynamics.42(11):5475-5484. PMID: 37418175Barua SA, Choudhary RK, Gawde J, Mishra N, Varma AK (2024)
- 2023Evaluation of pathogenicity and structural alterations for the mutations identified in the conserved region of the C‑terminal kinase domain of Human-Ribosomal S6 Kinase 1. ACS Omega.
Chikhale V, Goswami N, Khan MA, Borah P, Varma AK.
- 2022Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. International Journal of Biological Macromolecules. Macromolecules. 209: Part A:716-724
Khan MA, Siddiqui MQ, Kuligina E, Varma AK
In Silico and Structure-Based Assessment of Similar Variants Discovered in Tandem Repeats of BRCT Domains of BRCA1 and BARD1 To Characterize the Folding Pattern, ACS Omega DOI: 10.1021/acsomega.2c04782Siddhartha A. Barua, Nabajyoti Goswami, Neha Mishra, Ulka U. Sawant, and Ashok K. Varma
In-silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2, Journal of Biomolecular Structure and Dynamics, (2022): DOI: 10.1080/07391102.2022.2148127Mudassar Ali Khan & Ashok K Varma
Multimodal approach to characterize the tetrameric form of human PML-RBCC domain and ATO-mediated conformational changes, Int J Biol Macromol, (2022), 223 468–478Suchita Dubey, Neha Mishra, Nabajyoti Goswami ,M. Quadir Siddiqui, Ashok K.Varma
Breast Cancer Is Significantly Associated with Cancers in The First- and Second-Degree Relatives in Ethnic Mizo-Mongoloid Population, Northeast India; Natl J Community Med 2022;13(9):606-611Doris Zodinpuii, Jeremy L Pautu, Bawitlung Zothankima, Lalfakzuala Khenglawt, Doris Lallawmzuali, Rebecca Lalmuanpuii, Lalfak zuali, Lalengkimi Ralte, Rajendra B Muthukumaran, Ashok K Varma, John Zothanzama, Nachimuthu Senthil Kumar
- 2021
- 2020miRNA-mRNA profiling reveals prognostic impact of SMC1A expression in acute myeloid leukemia. Oncol Res. 2020 Feb 14. doi: 10.3727/096504020X15816752427321
Gadewal N, Kumar R, Aher S, Gardane A, Gaur T, Varma AK, Khattry N, Hasan SK
Comprehensive analysis of low molecular weight serum proteome enrichment for mass spectrometric studies. ACS OMEGA. 5(44): 28877-2888. PMID: 33195941Das L, Murthy V, Varma AK (2020)
Genetic ablation of pregnancy zone protein promotes breast cancer progression by activating TGF-â/SMAD signaling. Breast Cancer Research and Treatment. PMID: 33057846Kumar R, Kuligina E, Sokolenko A, Siddiqui Q, Gardi N, Gupta S, Varma AK, Hasan SK (2020)
- 2019Exome sequencing study of Russian breast cancer patients suggests a predisposing role for USP39. Breast Cancer Res Treat. 2019 Nov 21. doi: 10.1007/s10549-019-05492-6. PMID: 31754952
Kuligina ES, Sokolenko AP, Bizin IV, Romanko AA, Zagorodnev KA, Anisimova MO, Krylova DD, Anisimova EI, Mantseva MA, Varma AK, Hasan SK, Ni VI, Koloskov AV, Suspitsin EN, Venina AR, Aleksakhina SN, Sokolova TN, Milanović AM, Schürmann P, Prokofyeva DS, Bermisheva MA, Khusnutdinova EK, Bogdanova N, Dörk T, Imyanitov EN
Effect of single amino acid mutations on C-terminal domain of breast cancer susceptible protein 1, International Journal of Bioinformatics Research and Applications (IJBRA), 305-323 Vol. 15, No. 4, 2019, DOI: 10.1504/IJBRA.2019.103783Satish Kumar; Lingaraja Jena; Maheswata Sahoo; Kanchan Mohod; Sangeeta Daf; Ashok K. Varma
Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans. J Biomol Struct Dyn. 2019 Jan 27:1-10. doi: 10.1080/07391102.2019.1568916Sharma DK, Siddiqui MQ, Gadewal N, Choudhary RK, Varma AK, Misra HS, Rajpurohit YS
- 2018Biophysical evaluation to categories pathogenicity of cancer predisposing mutations identified in the BARD1BRCT domain, RSC Advances, 2018, 8, 34056 – 34068
Choudhary RK, Siddiqui MQ, Gadewal N, Senthil Kumar N, Kuligina ES , Varma AK
Identification and characterization of GRIP domain Golgin PpImh1 from Pichia pastoris. Yeast. 2018 Aug;35(8):499-506. doi: 10.1002/yea.3317.Jain BK, Thapa PS, Varma A, Bhattacharyya D
- 2017Studies of protein-protein interactions in Fanconi anemia pathway to unravel the DNA interstrand crosslink repair mechanism. Int J Biol Macromol. 2017 Nov;104(Pt A):1338-1344
Siddiqui MQ, Rajpurohit YS, Thapa PS, Maurya GK, Banerjee K, Khan MA, Panda P, Hasan SK, Gadewal N, Misra HS, Varma AK
Structural basis to stabilize the domain motion of BARD1-ARD BRCT by CstF50. Sci Rep. 2017 Jun 20;7(1):3849. doi: 10.1038/s41598-017-03816-4Choudhary RK, Siddiqui MQ, Thapa PS, Gadewal N, Nachimuthu SK, Varma AK
Structural and biophysical properties of h-FANCI ARM repeat protein. J Biomol Struct Dyn. 2017 Nov;35(14):3032-3042Siddiqui MQ, Choudhary RK, Thapa P, Kulkarni N, Rajpurohit YS, Misra HS, Gadewal N, Kumar S, Hasan SK, Varma AK
- 2016Functional Basis and Biophysical Approaches to Characterize the C-Terminal Domain of Human-Ribosomal S6 Kinases-3. Cell Biochem Biophys. 2016 Sep;74(3):317-25
Jagilinki BP, Choudhary RK, Thapa PS, Gadewal N, Hosur MV, Kumar S, Varma AK
Structural basis to characterise transactivation domain of BRCA1. J Biomol Struct Dyn. 2016 Mar 1:1-7Yadav LR, Biswal MN, Hosur MV, Kumar NS, Varma AK
Multimodal approach to explore the pathogenicity of BARD1, ARG 658 CYS, and ILE 738 VAL mutants. J Biomol Struct Dyn. 2016 Jul;34(7):1533-44Choudhary RK, Vikrant, Siddiqui QM, Thapa PS, Raikundalia S, Gadewal N, Kumar NS, Hosur MV, Varma AK
- 2015Virtual screening for potential inhibitors of high-risk human papillomavirus 16 E6 protein. Kumar S, Jena L, Mohod K, Daf S, Varma AK. Interdiscip Sci. (2015) Feb 6
S Kumar, L Jena, K Mohod, S Daf, Ashok K Varma
In Silico Docking to Explicate Interface between Plant-Originated Inhibitors and E6 Oncogenic Protein of Highly Threatening Human Papillomavirus 18. Genomics Inform. 2015 Jun;13(2):60-7Kumar S, Jena L, Sahoo M, Kakde M, Daf S, Varma AK
Functional assessment of intrinsic disorder central domains of BRCA1. J Biomol Struct Dyn. 2015 Jan 23:1-10Yadav LR, Rai S, Hosur MV, Varma AK
- 2014Tetrameric ZBRK1 DNA binding domain has affinity towards cognate DNA in absence of Zinc ions, Biochem Biophys Res Commun (2014) 18;450(1):283-8
Lumbini R Yadav, Mahamaya N. Biswal, Vikrant, M.V Hosur, Ashok K Varma
Mislocalization of BRCA1-complex due to ABRAXAS Arg361Gln mutation. J Biomol Struct Dyn. (2014) 8:1-11Vikrant, Kumar R, Siddiqui Q, Singh N, Waghmare SK, Ashok K Varma
Conserved Residues at the MAPKs Binding Interfaces that Regulate Transcriptional Machinery. Journal of Biomolecular Structure and Dynamics (2014) 1-28.Bhanu P Jagilinki, Nikhil Gadewal, Harshal Mehta, Hafiza Mahadik, Vikrant, Anamika Pandey, Ulka Sawant, Prasad A Wadegaonkar, Peyush Goyal, Satish Kumar, Ashok K Varma
Role of MERIT40 in stabilization of BRCA1-complex: A protein-protein interaction study. Biochem Biophys Research Communication (2014). 446, 1139–1144Vikrant, Ulka Sawant, Ashok K Varma
Elucidating Molecular Interactions of Natural Inhibitors with HPV-16 E6 Oncoprotein through Docking Analysis. Genomics Inform (2014). 12(2):64-70.Kumar S, Jena L, Galande S, Daf S, Mohod K, Ashok K Varma
- 2013Preliminary crystallographic studies of BRCA1 BRCT–ABRAXAS complex, Acta Cryst. (2013). F69, 1401–1404
Dilip C. Badgujar, Ulka Sawant,Vikrant, Lumbini Yadav, M. V. Hosur and Ashok K. Varma,
hpvPDB: An Online Proteome Reserve for Human Papillomavirus. Genomics Inform. 2013 Dec;11(4):289-91Kumar S, Jena L, Daf S, Mohod K, Goyal P, Ashok K. Varma
Over-expression, purification and isotopic labeling of a tag-less human glucose-dependent insulinotropic polypeptide (hGIP) (2013) 3 Biotech. 13205-013-0181R.C. Chandarana, Vikrant, Ashok K Varma, A. Saran A, E.C. Coutinho, J. D'souza
Structural and Functional Characterization of MERIT40 for its DNA Repair Function J Biomol Struct Dyn. 2013Vikrant, Disha Shah, Pallavi Nakhwa, Dilip C Badgujar, Khushboo K.S Rathore, Ashok K Varma
Structural and Functional Implication of RAP80 Δ81Glu Mutation, PLoS ONE 8(9):e72707 (2013)Vikrant, Rajan Kumar, Lumbini R Yadav, Pallavi Nakhwa, Sanjeev K Waghmare, Ashok K Varma
Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1, , Bioinformatics and Biology Insights, 7 1–18 (2013)Ajit K. Sharma. Abhilasha Mansukh, Ashok K Varma, Nikhil Gadewal and Sanjay Gupta
- 2012Targeting Pim-1 Kinase for Potential Drug-Development Int. J. Computational Biology and Drug Design, Vol. 5(2), 137, (2012)
Gadewal, N, Ashok K. Varma
Pathogenicity of Mutations Discovered in BRCA1 BRCT Domains is Characterized by Destabilizing the Hydrophobic Interactions, J Cancer Sci Ther, Volume 4(11) 386-393 (2012)Dilip C Badgujar, Ulka Sawant, Hafiza Mahadik, Nikhil Gadewal and Ashok K Varma
- 2010Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing. PLoS ONE, 5(8); e12029, (2010)
Patil R, Das S, Stanley A, Yadav L, Sudhakar A, Ashok K. Varma
Oxaliplatin-Mediated Inhibition of Survivin Increases Sensitivity of Head and Neck Squamous Cell Carcinoma Cell Lines to Paclitaxel. Curr Cancer Drug Targets. 10(7): 660-669, (2010)Khan Z, Khan N, Ashok K. Varma, Tiwari RP, Mouhamad S, Prasad GB, Bisen PS:
- 2009Validation of Different Systems for Tumstatin Expression and its in-vitro and iv -vivo Activities. J Cancer Sci Ther. 2010 Jul 2; 8-18 (2009)
Boosani CS, Ashok K. Varma, Sudhakar A
- 2007A novel loop domain in superantigens extends their T cell receptor recognition site. J Mol Biol. 371(1):210-21, 2007
Günther S, Ashok K. Varma, Moza B, Kasper KJ, Wyatt AW, Zhu P, Rahman AK, Li Y, Mariuzza RA, McCormick JK, and Sundberg EJ
Crystal structure of the BARD1 BRCT domains. Biochemistry. 46(26):7706-12,2007Birrane G, Ashok K. Varma, Soni A and Ladias JA
Crystal structure of the streptococcal superantigen SpeI and functional role of a novel loop domain in T cell activation by group V superantigens. J Mol Biol. 367(4):925-34, 2007Brouillard JN, Günther S, Ashok K. Varma, Gryski I, Herfst CA, Rahman AK, Leung DY, Schlievert PM, Madrenas J, Sundberg EJ and McCormick JK
Structural basis of T-cell specificity and activation by the bacterial superantigen TSST-1. EMBO J. 26(4):1187-97, 2007Moza B, Ashok K. Varma, Buonpane RA, Zhu P, Herfst CA, Nicholson MJ, Wilbuer AK, Seth NP, Wucherpfennig KW, McCormick JK, Kranz DM and Sundberg EJ
- 2005Structural basis for cell cycle checkpoint control by the BRCA1-CtIP complex. Biochemistry. 44(33):10941-6, 2005
Ashok K. Varma, Brown RS, Birrane G and Ladias JA
Structural basis for cell cycle checkpoint control by the BRCA1-CtIP complex. Biochemistry. 44(33):10941-6, 2005.Ashok K. Varma, Brown RS, Birrane G and Ladias JA
- 2002Sulfinyl group as an intramolecular neuclophile, , J.Org.Chem.(2002) 67(16) 5838-41
S. Raghavan, S.R.Reddy, K.A.Tony, C.N. Kumar, Ashok K. Varma, Ashwani Nangia
- 2001Hydrogen bonding in two tetracyclic indole alkaloids, Acta Crystallogr C. (2001) 57; 97-9
Ashok K. Varma, A. Nangia, G.R.Desiraju, V.S. Giri, P. Jaisankar