Name:Raghu M. Yennamalli, Ph.D.
Designation: Assistant Professor (Grade II)
Contact Info: 2nd Floor, VivekanadaBhavan,
Department of Biotechnology and Bioinformatics,
Jaypee University of Information Technology.
Waknaghat, P.O. Waknaghat
TehKandaghat, Distt. Solan.
Himachal Pradesh -173 234.
Educational Info
2008 Ph. D. in Computational Biology and Bioinformatics, Jawaharlal Nehru University, India.Advisor: Dr. Naidu Subbarao
2003 Advance Post Graduate Diploma in Bioinformatics, Jawaharlal Nehru University, India.Advisor: Dr. Andrew Lynn
2002 M. Sc. in Microbial Gene Technology, Madurai Kamaraj University, India.
Advisor: Dr. S. Shanmugasundaram
2000 B. Sc. in Microbiology, University of Madras, India
Dr. Yennamalli is a structural and computational biologist with a more than a decade of experience in predictive modelling and biomolecular simulation projects. Dr. Yennamalli’sskills involve molecular docking, molecular dynamics simulation, coarse grained modelling, machine learning, data mining, data analytics, and molecular modelling. He hascontributed to multiple diverse projects that focus on basic and applied sciences. His experience in computational structural biology is critical in finding answers to bigger questions in life.
Research Interests
Cellulases for biofuel production, thermostability of proteins, Natural Product Biosynthesis, protein-ligand interactions, Elastic Network Models, Gene expression networks
Molecular modeling techniques: homology modeling, molecular dynamics simulation (Gromacs, NAMD), molecular docking (AutoDock, DOCK, Gold, FlexX, Glide)
Publications
1.Chauhan D, Srivastava PA, Yennamalli RM, Priyadarshini R
Draft Genome Sequence of Deinococcusindicus DR1, a Novel Strain Isolated from a Freshwater Wetland
Genome Announcements 2017 5(31): e00754-17.
(Scopus CiteScore: 0.41)
2. Vij A, Yennamalli RM, Changotra H.
Non-synonymous Single Nucleotide Polymorphisms of ATG5 destabilize ATG12-ATG5-ATG16L1 complex: an enzyme with E3 like activity of Ubiquitin conjugation system.
MetaGene2017 13: 38-47.
(Scopus CiteScore: 1.55)
3. Srivastava PA, Kalra S, Yennamalli RM.
Structural Bioinformatics and Big Data Analytics: A mini-review.
International Journal of Computational Biology 2017 6 (1): 25-30.
4. Yennmalli RM, Kalra S, Srivastava PA, Garlapati VK.
Computational Tools and Resources for CRISPR/Cas 9 Genome Editing Method:Mini Review.
MOJ Proteomics and Bioinformatics20175(4): 00164.
5. Chang CY, Lohman JR, Cao H, Tan K, Rudolf JD, Ma M, Xu W, Bingman CA, Yennamalli RM, Bigelow L, Babnigg G, Yan X, Joachimiak A, Phillips GN Jr, Shen B.
Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase that Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate in Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomycesglobisporus
Biochemistry 2016 55(36):5142-5154.
(SCI IF:2.938) (Scopus CiteScore: 2.80)
6. Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L.
A clade-specific Arabidopsis gene connects primary metabolism and senescence.
Frontiers in Plant Science2016, 7: 983
(SCI IF: 4.495) (Scopus CiteScore: 4.52)
7. Gautam LK, Yennamalli RM*, Rathore JS*.
Implication on the function of novel Xn-relE toxinstructure of Xenorhabdusnematophila using Homology modeling.
Current Bioinformatics 2016, 11(3): (*Corresponding author)
(SCI IF: 0.77) (Scopus CiteScore: 0.60)
8. Huang T, Chang CY, Lohman J, Rudolf J, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN Jr.
Crystal Structure of SgcJ, An NTF2-Like Superfamily Protein Involved in Biosynthesis of the 9-Membered Enediyne Antitumor Antibiotic C-1027.
The Journal of Antibiotics2016, Nature Publication Group 69(10):731-740.
(SCI IF: 2.237) (Scopus CiteScore: 2.16)
9.Chauhan M*, Yennamalli RM*, Garlapati VK.
Biochemical and Molecular Characterization of a unique lipase from Staphylococcus arlettae JPBW1.Engineering in Life Sciences 2016 16(8):762–768 (* Equal authors)
(SCI IF: 2.168) (Scopus CiteScore: 2.10)
10. Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson J, Phillips. GN, Jr.
Structural Dynamics of a Methionineγ-Lyase for Calicheamicin Biosynthesis: Rotation of the Conserved Tyrosine Stacking with PyridoxalPhosphate
Structural Dynamics2016 3, 034702
(SCI IF: 2.968) (Scopus CiteScore: 2.41)
11. Singh S, Michalska K, Bigelow L, Endres M, Kharel MK, Babnigg G, Yennamalli RM, Bingman CA, Joachimiak A, Thorson JS, Phillips GN Jr.
Structural Characterization of CalS8, a TDP-alpha-D-Glucose Dehydrogenase Involved in CalicheamicinAminodideoxypentose Biosynthesis.
Journal of Biological Chemistry 2015 Oct 23; 290(43):26249-26258.
(SCI IF: 2.082) (Scopus CiteScore: 4.17)
12. Auldridge ME, Cao H, SenS, FranzLP, BingmanCA, Yennamalli RM, Phillips GN Jr, Mead D, SteinmetzEJ
LucY: a versatile new fluorescent reporter protein
PLOS One. 2015 10(4):e0124272.
(SCI IF: 2.806) (Scopus CiteScore: 3.11)
13. Weerth RS, Michalska K, Bingman CA, Yennamalli RM, Li H, Jedrzejczak R, Wang F, Babnigg G, Joachimiak A, Thomas MG, Phillips GN Jr.
Structure of a cupin protein Plu4264 from Photorhabdusluminescens subsp. laumondii TTO1 at 1.35Å resolution.
Proteins: Structure, Function, and Bioinformatics. 2015 Feb; 83(2):383-388
(SCI IF: 2.289) (Scopus CiteScore: 2.25)
14.*Yennamalli RM, *Book AJ,*Takasuka TE, Currie CR, Phillips GN, Fox BG.
Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases.
Biotechnology for Biofuels 2014 7:109 (*Equal authors)
(SCI IF: 5.203) (Scopus CiteScore: 5.89)
15. Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S,YennamalliRM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN Jr, Thorson JS.
Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19.
ACS Chemical Biology 2014 Oct; 9(10):2347-2358.
(SCI IF: 4.995) (Scopus CiteScore: 4.90)
16. Yennamalli RM, Arangarasan R, Bryden A, Gleicher M, Phillips GN.
Using commodity HDTV for Collaborative Structural Biology
Journal of Applied Crystallography 2014 May; 29: 47 (Pt 3): 1153-1157
(SCI IF: 2.495) (Scopus CiteScore: 2.51)
17. Ilgu M, Fulton BD, Yennamalli RM, Lamm MH, Sen TZ, Nilsen-Hamilton M.
An Adaptable Pentaloop Defines a Robust Neomycin-B RNA Aptamer with Conditional Ligand Bound Structures.
RNA 2014 Jun; 20(6): 815-824.
(SCI IF: 4.39) (Scopus CiteScore: 3.69)
18. Yennamalli RM, Rader AJ, Kenny AJ, Wolt JD, Sen TZ.
Endoglucanases: Insights into Thermostability for Biofuel Applications
Biotechnology for Biofuels2013 6:136
(SCI IF: 5.203) (Scopus CiteScore: 5.89)
19. Wang F, Zhou M, Singh S, Yennamalli RM, Bingman CA, Thorson JS, Phillips GN Jr.
Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis.
Proteins: Structure, Function, and Bioinformatics 2013 Jul; 81(7): 1277-1282.
(SCI IF: 2.289) (Scopus CiteScore: 2.25)
20. Rader AJ,Yennamalli RM, Harter AK, Sen TZ.
A rigid network of long-range contacts increases thermostability in a mutant endoglucanase.
Journal of Biomolecular Structure and Dynamics 2012 Jun; 30(6): 628-637.
(SCI IF: 3.123) (Scopus CiteScore: 1.94)
21. Yennamalli RM, Wolt JD, Sen TZ.
Dynamics of endoglucanase catalytic domains: Implications towards thermostability.
Journal of Biomolecular Structure and Dynamics 2011 Dec; 29(3): 509-526.
(SCI IF: 3.123) (Scopus CiteScore: 1.94)
22. Yennamalli RM, Rader AJ, Wolt JD, Sen TZ.
Thermostability in Endoglucanases is Fold-specific.
BMC Structural Biology 2011 11:10.
(SCI IF: 1.771) (Scopus CiteScore: 1.72)
23. Khan SN, Yennamalli R, Subbarao N, Khan AU.
Mitoxantrone Induced Impediment of HistoneAcetylation and Structural Flexibility of the Protein.
Cell Biochemistry and Biophysics 2010 Jul; 60(3): 209-218.
(SCI IF: 1.320) (Scopus CiteScore: 1.51)
24. Hambarde S, Yennamalli RM, Subbarao N, Chandna S.
Predictive inference on cytoplasmic and mitochondrial thioredoxinperoxidases in the highly radioresistantLepidopteran insect Spodopterafrugiperda.
Bioinformation. 2010 Mar 31; 4(9):399-404.
(IF: 0.60)
25. *Yennamalli RM, *Das S, *Vishnoi A, Gupta P, Bhattacharya A.
Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains.
Journal of Biosciences 2009 Sep; 34(3):397-404. (* Equal authors)
(SCI IF: 1.422) (Scopus CiteScore: 1.43)
26. Kampmann T, Yennamalli R, Campbell P, Stoermer MJ, Fairlie DP, Kobe B, Young PR.
In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses.
Antiviral Research 2009 Dec; 84(3):234-241.
(SCI IF: 4.271) (Scopus CiteScore: 4.50)
27. Vashist J, Vishvanath, Kapoor R, Kapil A, Yennamalli R, Subbarao N, Rajeswari MR
Interaction of nalidixic acid and ciprofloxacin with wild type and mutated quinolone-resistance-determining region of DNA gyrase A.
Indian Journal of Biochemistry and Biophysics 2009 Apr; 46(2):147-153.
(SCI IF: 0.958) (Scopus CiteScore: 0.70)
28. YennamalliR,Subbarao N, Kampmann T, McGeary RP, Young PR, Kobe B.
Identification of novel target sites and an inhibitor of the dengue virus E protein.
Journal of Computer-Aided Molecular Design 2009 Jun; 23(6):333-341.
(SCI IF: 3.028) (Scopus CiteScore: 3.23)
29. Khan SN, Islam B, Yennamalli R, Zia Q, Subbarao N, Khan AU.
Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin.
Journal of Pharmaceutical and Biomedical Analysis 2008 Dec 1; 48(4):1096-1104.
(SCI IF: 3.255) (Scopus CiteScore: 3.24)
30. Khan SN, Islam B, Yennamalli R, Sultan A, Subbarao N, Khan AU.
Interaction of mitoxantrone with human serum albumin: spectroscopic and molecular modeling studies.
European Journal of Pharmaceutical Sciences 2008 Dec 18; 35(5):371-382.
(SCI IF: 3.756) (Scopus CiteScore: 4.20)
31. Mueller DS, Kampmann T, Yennamalli R, Young PR, Kobe B, Mark AE.
Histidineprotonation and the activation of viral fusion proteins.
Biochemical Society Transactions 2008 Feb; 36(Pt 1):43-45.
(SCI IF: 2.765) (Scopus CiteScore: 2.99)
General Articles
1. Recent trends and developments in bioinformatics: challenges and opportunities
Ahmed Moussa, Brigitte Vannier, RagothamanYennamalli,Tiratha Raj Singh.
For special issue on Bioinformatics in CSI Communications, published by Computer Society of India, October 2016, 40(7):28-31.
Honors and Awards
●Awarded the prestigious Bioenergy-Awards for Cutting Edge Research (B-ACER) Fellowship Program 2017 supported by the Department of Biotechnology, Govt. of India, and the Indo-U.S. Science and Technology Forum (IUSSTF) for the research work "Systems level analysis of Lytic Polysaccharide Monooxygenases and their involvement in degradation of recalcitrant crystalline cellulose" at University of Wisconsin-Madison, hosted by Prof. Brian Fox.
●Manuscript titled “Thermostability in Endoglucanases is Fold-specific.” in BMC Structural Biology 2011 is
●Awarded 2006 Endeavour Australia Cheung Kong award for Asian scholars to undertake part of PhD program at The University of Queensland, Brisbane in 2006.
●Awarded Senior Research Fellowship from Indian Council of Medical Research in 2005.
●Nominated for the Jawaharlal Nehru University – The University of Queensland student exchange program in 2004 funded by DEST, Australian government.
●Awarded the Junior Research Fellowship from Indian Council of Medical Research in 2003.
●Awarded scholarship by Department of Biotechnology, Govt. of India for Advanced Post Graduate Diploma in Bioinformatics, 2002.
●Won Silver Medal at National Children’s Science Congress, Guwahati, Assam 1996.
Invited Talks and Workshops
●Invited to deliver lectures and conducting hands-on practical on ““Application of Bioinformatics Tools in Plant Sciences” at Dr Y S Parmar University of Horticulture and Forestry,Nauni in August 24-25th 2017.
●Invited to deliver lectures and conducting hands-on practical on “Molecular modelling for disease causing proteins and drug targeting” at Himachal Pradesh University, Shimla, Himachal Pradesh in November 2016.
●Talk titled “Enzyme discovery for natural product biosynthesis” at 69th Southwest Regional Meeting of the American Chemical Society, November 2013, in Waco, Texas.
●Talk titled “Understanding Thermostability in Endoglucanases for Biofuel Applications” at Jawaharlal Nehru University, New Delhi in January 2011.
●Conducted workshop at “National workshop in Drug Designing” at Birla Insititute of Scientific Research, Jaipur in October 2008.
●Conducted hands-on workshop on Bioinformatics at Madurai Kamaraj University, Madurai in August 2008.
●Invited to deliver lectures and conducting hands-on practicals on “Applications of Structural Bioinformatics tools for Biologists” at Himachal Pradesh University, Shimla, Himachal Pradesh in September 2007.
●Invited to deliver lectures and conducting hands-on practicals on “Applications of Structural Bioinformatics tools for Biologists” at Guru Nanak Dev University, Amritsar, Punjab in March 2007.
●Invited to deliver lectures and conducting hands-on practicals on “Usage of Bioinformatics tools for Biologists” at Himachal Pradesh University, Shimla, Himachal Pradesh in September 2005.