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Bioinformatics, Computational Biology, Structural Dynamics
India

Biography

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’s skills involve molecular docking, molecular dynamics simulation, coarse grained modelling, machine learning, data mining, data analytics, and molecular modelling. He has contributed 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.

Activities

Employment (4)

Rice University: Houston, TX, US

2012-09 to 2014-06 | Postdoctoral Research Associate (Biosciences)
Employment
Source: Self-asserted source
Ragothaman Yennamalli

University of Wisconsin Madison: Madison, WI, US

2011-10 to 2012-09 | Postdoctoral Research Associate (Biochemistry)
Employment
Source: Self-asserted source
Ragothaman Yennamalli

Iowa State University: Ames, IA, US

2009-07 to 2011-09 | Postdoctoral Research Associate (GDCB)
Employment
Source: Self-asserted source
Ragothaman Yennamalli

Jawaharlal Nehru University: New Delhi, Delhi, IN

2008-10 to 2009-02 | Research Assistant (Center for Computational Biology and Bioinformatics)
Employment
Source: Self-asserted source
Ragothaman Yennamalli

Education and qualifications (4)

Jawaharlal Nehru University: New Delhi, Delhi, IN

2003 to 2008 | PhD (Center for Computational Biology and Bioinformatics)
Education
Source: Self-asserted source
Ragothaman Yennamalli

Jawaharlal Nehru University: New Delhi, Delhi, IN

2002 to 2003 | PG Diploma in Bioinformatics (Center for Computational Biology and Bioinformatics)
Education
Source: Self-asserted source
Ragothaman Yennamalli

Madurai Kamaraj University: Madurai, Tamil Nadu, IN

2000 to 2002 | M.Sc. Microbial Gene Technology (Microbial Technology)
Education
Source: Self-asserted source
Ragothaman Yennamalli

University of Madras: Chennai, Tamil Nadu, IN

1997 to 2000 | B.Sc (Microbiology)
Education
Source: Self-asserted source
Ragothaman Yennamalli

Professional activities (5)

International Society for Computational Biology: Leesburg, Virginia, US

Membership
Source: Self-asserted source
Ragothaman Yennamalli

Indian Biophysical Society: Mumbai, Maharashtra, IN

Membership
Source: Self-asserted source
Ragothaman Yennamalli

Biophysical Society: Rockville, Maryland, US

Membership
Source: Self-asserted source
Ragothaman Yennamalli

International Society for Computational Biology: La Jolla, CA, US

2022 to present | Chair (Publication Committee)
Service
Source: Self-asserted source
Ragothaman Yennamalli

Asia Pacific Bioinformatics Network: Singapore, SG

2024 to 2026 | Executive Committee Member
Invited position
Source: Self-asserted source
Ragothaman Yennamalli

Funding (5)

Development of a mechanoenzymatic approach for improved production of chito-oligosaccharides from recalcitrant chitin waste

2024-10 to 2027-09 | Grant
DBT (New Delhi, IN)
Source: Self-asserted source
Ragothaman Yennamalli

Indian Knowledge System - AICTE

2023-01 to 2025-12 | Grant
All India Council for Technical Education (New Delhi, IN)
Source: Self-asserted source
Ragothaman Yennamalli

Unique innate-immunity genomic signatures identfication using Immunoinformatics

2022 to 2025 | Grant
ICAR - National Agricultural Science Fund (New Delhi, IN)
Source: Self-asserted source
Ragothaman Yennamalli

UGC Grant

2021 to 2023 | Grant
University Grants Commission (New Delhi, IN)
Source: Self-asserted source
Ragothaman Yennamalli

Systems level analysis of Lytic Polysaccharide Monooxygenases and their involvement in degradation of recalcitrant polysaccharides

Award
Indo-US Science Technology Forum (New Delhi, IN)
Source: Self-asserted source
Ragothaman Yennamalli

Works (50 of 71)

Items per page:
Page 1 of 2

Immunoinformatics: A Veritable Toolbox for Livestock Omics and Veterinomics

OMICS: A Journal of Integrative Biology
2025-02-01 | Journal article
Contributors: Ragothaman M. Yennamalli; Suneel K. Onteru
Source: check_circle
Crossref

Genetic Basis of Immunity in Indian Cattle as Revealed by Comparative Analysis of Bos Genome

2024-12-18 | Preprint
Contributors: Menaka Thambiraja; Shukkruthi K. Iyengar; Brintha Satishkumar; Sai Rohith Kavuru; Aakanksha Katari; Dheer Singh; Suneel K. Onteru; Ragothaman M. Yennamalli
Source: check_circle
Crossref

Genetic basis of immunity in Indian cattle as revealed by comparative analysis ofBosgenome

2024-12-10 | Preprint
Contributors: Menaka Thambiraja; Shukkruthi K. Iyengar; Brintha Satishkumar; Sai Rohith Kavuru; Aakanksha Katari; Dheer Singh; Suneel K. Onteru; Ragothaman M. Yennamalli
Source: check_circle
Crossref

Genetic heterogeneity and respiratory chain enzyme analysis in pediatric Indian patients with mitochondrial disorder: Report of novel variants in POLG1 gene and their functional implication using molecular dynamic simulation

Mitochondrion
2024-03 | Journal article
Contributors: Debolina Saha; Sonam Kothari; Shilpa Duttaprasanna Kulkarni; Menaka Thambiraja; Ragothaman M Yennamalli; Dhanjit K Das
Source: check_circle
Crossref

Structure predictions and functional insights into Amidase_3 domain containing N-acetylmuramyl-L-alanine amidases from Deinococcus indicus DR1.

BMC microbiology
2024-03 | Journal article
Contributors: Modi M; Thambiraja M; Cherukat A; Yennamalli RM; Priyadarshini R
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Targeting the Bottlenecks in Levan Biosynthesis Pathway in Bacillus subtilis and Strain Optimization by Computational Modeling and Omics Integration

OMICS: A Journal of Integrative Biology
2024-02-01 | Journal article
Contributors: Aruldoss Immanuel; Ragothaman M. Yennamalli; Venkatasubramanian Ulaganathan
Source: check_circle
Crossref

Waste to drugs: identification of pyrolysis by-products as antifungal agents against Cryptococcus neoformans

Journal of Biomolecular Structure and Dynamics
2023-12-29 | Journal article
Contributors: Srividhya Krishnan; Krishnakant Gupta; Subramaniyasharma Sivaraman; Ponnusami Venkatachalam; Ragothaman M. Yennamalli; Saravanan Ramiah Shanmugam
Source: check_circle
Crossref

Surface exposed and charged residues drive thermostability in fungi.

Proteins
2023-11 | Journal article
Contributors: Senthilkumar S; Mahesh S; Jaisankar S; Yennamalli RM
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Key essential oil components delocalize Candida albicans Kar3p and impact microtubule structure.

Microbiological research
2023-04 | Journal article
Contributors: Shahina Z; Yennamalli RM; Dahms TES
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity

2023-01 | Preprint
Contributors: Sahu D; Gupta C; Yennamalli RM; Sharma S; Roy S; Hasan S; Gupta P; Sharma VK; Kashyap S; Kumar S et al.
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity

2022-12 | Preprint
Contributors: Sahu D; Gupta C; Yennamalli R; Sharma S; Roy S; Hasan S; Gupta P; Sharma VK; Kashyap S; Kumar S et al.
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Structural and functional mapping of <i>ars</i> gene cluster in <i>Deinococcus indicus</i> DR1.

Computational and structural biotechnology journal
2022-12 | Journal article
Contributors: Ranganathan S; Sethi D; Kasivisweswaran S; Ramya L; Priyadarshini R; Yennamalli RM
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

'Targeting' the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets.

Frontiers in cellular and infection microbiology
2022-10 | Journal article
Contributors: Ravichandran S; Avatapalli S; Narasimhan Y; Kaushik KS; Yennamalli RM
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

‘Targeting’ the Search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets

2022-08 | Preprint
Contributors: Ravichandran S; Avatapalli SS; Narasimhan Y; Kaushik KS; Yennamalli RM
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Coarse grained modelling highlights the binding differences in the two different allosteric sites of the Human Kinesin EG5 and its implications in inhibitor design.

Computational biology and chemistry
2022-06 | Journal article
Contributors: Alexandar SP; Yennamalli RM; Ulaganathan V
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to <i>Corynebacterium striatum</i>, an Emerging Pathogen.

Frontiers in cellular and infection microbiology
2021-12 | Journal article
Contributors: Mhade S; Panse S; Tendulkar G; Awate R; Narasimhan Y; Kadam S; Yennamalli RM; Kaushik KS
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes

2021-12-29 | Preprint
Contributors: Sankar Mahesh; Deepa Sethi; Richa Priyadarshini; Ragothaman M. Yennamalli
Source: check_circle
Crossref

Identification of a low CO2 responsive mutant from chemical mutagenesis of Setaria viridis shows that reduced carbonic anhydrase severely limits C4 photosynthesis.

Journal of experimental botany
2021-02 | Journal article
Contributors: Chatterjee J; Coe RA; Acebron K; Thakur V; Yennamalli RM; Danila F; Lin HC; Balahadia CP; Bagunu E; Padhmapreiya POS et al.
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis

OpenAlex
2021-02-02 | Other
Contributors: Jolly Chatterjee; Robert A. Coe; Kelvin Acebron; Vivek Thakur; Ragothaman Yennamalli; Florence Danila; Hsiang‐Chun Lin; Christian Paolo Balahadia; Efren Bagunu; Preiya P O S Padhma et al.
Source: check_circle
DataCite

A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis

OpenAlex
2021-02-02 | Other
Contributors: Jolly Chatterjee; Robert A. Coe; Kelvin Acebron; Vivek Thakur; Ragothaman Yennamalli; Florence Danila; Hsiang‐Chun Lin; Christian Paolo Balahadia; Efren Bagunu; Preiya P O S Padhma et al.
Source: check_circle
DataCite

DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus

Frontiers in microbiology
2021-01 | Journal article
Contributors: Pal P; Modi M; Ravichandran S; Yennamalli R; Priyadarshini R
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Identification of nsSNPs of transcription factor E2F1 predisposing individuals to lung cancer and head and neck cancer

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
2020-05 | Journal article
Part of ISSN: 0027-5107
Contributors: Sanjay Singh; Ragothaman M. Yennamalli; Manish Gupta; Harish Changotra
Source: Self-asserted source
Ragothaman Yennamalli via Crossref Metadata Search

PreDSLpmo: A neural network-based prediction tool for functional annotation of lytic polysaccharide monooxygenases

Journal of Biotechnology
2020-01 | Journal article
Contributors: Pulkit Anupam Srivastava; Eric L. Hegg; Brian G. Fox; Ragothaman M. Yennamalli
Source: check_circle
Crossref

Random insertion transposon mutagenesis of Mycobacterium fortuitum identified mutant defective in biofilm formation

Biochemical and Biophysical Research Communications
2020-01 | Journal article
Contributors: Poonam Katoch; Kinam Gupta; Ragothaman M. Yennamalli; Jitendraa Vashistt; Gopal Singh Bisht; Rahul Shrivastava
Source: check_circle
Crossref

Arsenate Reductase (ArsC) of Deinococcus indicus DR1

modelarchive.org
2019 | Other
Contributors: Chauhan, Deepika; Srivastava, Pulkit Anupam; Agnihotri, Vidushi; Yennamalli, Ragothaman M; Priyadarshini, Richa
Source: check_circle
DataCite

Comprehensive evaluation of chitosan nanoparticle based phage lysin delivery system; a novel approach to counter S. pneumoniae infections

International Journal of Pharmaceutics
2019-11 | Journal article
Contributors: Vijay Singh Gondil; Taru Dube; Jiban J. Panda; Ragothaman M. Yennamalli; Kusum Harjai; Sanjay Chhibber
Source: check_circle
Crossref

Genome-wide mutagenesis of hepatitis C virus reveals genome ability to overcome detrimental mutations.

Journal of virology
2019-11 | Journal article
Contributors: Singh D; Soni S; Khan S; Sarangi AN; Yennamalli RM; Aggarwal R; Veerapu NS
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Structural basis of the strong cell-cell junction formed by cadherin-23.

The FEBS journal
2019-11 | Journal article
Contributors: Singaraju GS; Sagar A; Kumar A; Samuel JS; Hazra JP; Sannigrahi MK; Yennamalli RM; Ashish F; Rakshit S
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Cinnamate:CoA-ligase is involved in benzoate-derived biphenyl phytoalexin biosynthesis in Malus × domestica 'Golden Delicious' cell cultures.

The Plant journal : for cell and molecular biology
2019-08 | Journal article
Contributors: Teotia D; Gaid M; Saini SS; Verma A; Yennamalli RM; Khare SP; Ambatipudi K; Mir JI; Beuerle T; Hänsch R et al.
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central
grade
Preferred source (of 2)‎

Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1.

Frontiers in microbiology
2019-07 | Journal article
Contributors: Chauhan D; Srivastava PA; Ritzl B; Yennamalli RM; Cava F; Priyadarshini R
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions

3 Biotech
2019-04 | Journal article
Contributors: Poonam; Ragothaman M. Yennamalli; Gopal S. Bisht; Rahul Shrivastava
Source: check_circle
Crossref

Structure and function prediction of arsenate reductase from Deinococcus indicus DR1

Journal of Molecular Modeling
2019-01 | Journal article
Contributors: Deepika Chauhan; Pulkit A. Srivastava; Vidushi Agnihotri; Ragothaman M. Yennamalli; Richa Priyadarshini
Source: check_circle
Crossref

Network and structure based inference of functional single nucleotide polymorphisms associated with the TGFβ1 gene and its role in colorectal cancer (CRC)

Gene Reports
2018 | Journal article
EID:

2-s2.0-85043788158

Contributors: Shukla, A.; Yennamalli, R.M.; Singh, T.R.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Computational and in-vitro validation of natural molecules as potential Acetylcholinesterase inhibitors and neuroprotective agents.

Current Alzheimer research
2018-12 | Journal article
Contributors: Kumar A; Mehta V; Raj U; Varadwaj PK; Udayabanu M; Yennamalli RM; Singh TR
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region.

Journal of molecular graphics & modelling
2018-12 | Journal article
Contributors: Arora R; Bharval P; Sarswati S; Sen TZ; Yennamalli RM
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Application of Molecular Simulations Toward Understanding Cellulase Mechanisms

BioEnergy Research
2018-12-16 | Journal article
Contributors: Mansi Arora; Ragothaman M. Yennamalli; Taner Z. Sen
Source: check_circle
Crossref

Non-synonymous single nucleotide polymorphisms of ATG5 destabilize ATG12–ATG5/ATG16L1 complex: An enzyme with E3 like activity of ubiquitin conjugation system

Meta Gene
2017 | Journal article
EID:

2-s2.0-85018379675

Contributors: Vij, A.; Yennamalli, R.M.; Changotra, H.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Modified S-transform as a tool to identify secondary structure elements in RNA

Bio-Algorithms and Med-Systems
2017-12-20 | Journal article
Contributors: Nancy Singh; Sunil Datt Sharma; Ragothaman M. Yennamalli
Source: check_circle
Crossref

Molecular mechanism of cell-cell adhesion mediated by cadherin-23

2017-10 | Other
OTHER-ID:

PPR24254

Contributors: Singaraju GS; Kumar A; Samuel JS; Sagar A; Hazra JP; Sannigrahi MK; Yennamalli RM; Ashish FNU; Rakshit S
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central

Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a Freshwater Wetland.

Genome announcements
2017-08 | Journal article
Contributors: Chauhan D; Srivastava PA; Yennamalli RM; Priyadarshini R
Source: Self-asserted source
Ragothaman Yennamalli via Europe PubMed Central
grade
Preferred source (of 2)‎

A Clade-specific arabidopsis gene connects primary metabolism and senescence

Frontiers in Plant Science
2016 | Journal article
EID:

2-s2.0-84978203773

Contributors: Jones, D.C.; Zheng, W.; Huang, S.; Du, C.; Zhao, X.; Yennamalli, R.M.; Sen, T.Z.; Nettleton, D.; Wurtele, E.S.; Li, L.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Biochemical characterization and molecular modeling of a unique lipase from Staphylococcus arlettae JPBW-1

Engineering in Life Sciences
2016 | Journal article
EID:

2-s2.0-84977539626

Contributors: Chauhan, M.; Yennamalli, R.M.; Garlapati, V.K.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

Journal of Antibiotics
2016 | Journal article
EID:

2-s2.0-84992573771

Contributors: Huang, T.; Chang, C.-Y.; Lohman, J.R.; Rudolf, J.D.; Kim, Y.; Chang, C.; Yang, D.; Ma, M.; Yan, X.; Crnovcic, I. et al.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus

Biochemistry
2016 | Journal article
EID:

2-s2.0-84987630046

Contributors: Chang, C.-Y.; Lohman, J.R.; Cao, H.; Tan, K.; Rudolf, J.D.; Ma, M.; Xu, W.; Bingman, C.A.; Yennamalli, R.M.; Bigelow, L. et al.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Implication on the function of novel Xn-relE toxin structure of xenorhabdus nematophila using homology modeling

Current Bioinformatics
2016 | Journal article
EID:

2-s2.0-85010378579

Contributors: Gautam, L.K.; Yennamalli, R.M.; Rathore, J.S.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Staphylococcus aureus Capsular Polysaccharide D

modelarchive.org
2016 | Other
Contributors: Yennamalli, Ragothaman;Chauhan, Mamta;Garlapati, Vijay Kumar
Source: check_circle
DataCite

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

Structural Dynamics
2016 | Journal article
EID:

2-s2.0-84966713069

Contributors: Cao, H.; Tan, K.; Wang, F.; Bigelow, L.; Yennamalli, R.M.; Jedrzejczak, R.; Babnigg, G.; Bingman, C.A.; Joachimiak, A.; Kharel, M.K. et al.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier

Xenorhabdus nematophila RelE antitoxin

modelarchive.org
2016 | Other
Contributors: Gautam, Lalit Kumar;Yennamalli, Ragothaman M;Rathore, Jitendra Singh
Source: check_circle
DataCite

Xenorhabdus nematophila RelE toxin

modelarchive.org
2016 | Other
Contributors: Gautam, Lalit Kumar;Yennamalli, Ragothaman M;Rathore, Jitendra Singh
Source: check_circle
DataCite

LucY: A versatile new fluorescent reporter protein

PLoS ONE
2015 | Journal article
EID:

2-s2.0-84928404900

Contributors: Auldridge, M.E.; Cao, H.; Sen, S.; Franz, L.P.; Bingman, C.A.; Yennamalli, R.M.; Phillips, G.N.; Mead, D.; Steinmetz, E.J.
Source: Self-asserted source
Ragothaman Yennamalli via Scopus - Elsevier
Items per page:
Page 1 of 2

Peer review (14 reviews for 7 publications/grants)

Review activity for Biochemical and biophysical research communications. (2)
Review activity for Biologia. (1)
Review activity for Communications biology. (1)
Review activity for Current research in structural biology. (2)
Review activity for Journal of biosciences. (1)
Review activity for Microbial pathogenesis. (3)
Review activity for Phytomedicine. (4)