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A. Padhi · SciRah

Researcher profile · Semantic Scholar

A. Padhi

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A. Padhi — researcher profile on SciRah

h-index: 19
Works: 60
Citations: 1,286

Most-cited papers

Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2
P. Kalita, A. Padhi, Kam Y. J. Zhang, Timir Tripathi
2020Microbial Pathogenesis183 citations Open access
Semantic Scholar
Development of multi-epitope driven subunit vaccine against Fasciola gigantica using immunoinformatics approach.
P. Kalita, D. Lyngdoh, A. Padhi, Harish Shukla +1 more
2019International Journal of Biological Macromolecules77 citations
Semantic Scholar
High-throughput rational design of the remdesivir binding site in the RdRp of SARS-CoV-2: implications for potential resistance
A. Padhi, Rohit Shukla, Prakash Saudagar, Timir Tripathi
2020iScience72 citations Open access
Semantic Scholar
Unraveling the mechanism of arbidol binding and inhibition of SARS-CoV-2: Insights from atomistic simulations
A. Padhi, Aniruddha Seal, J. M. Khan, M. Ahamed +1 more
2020European Journal of Pharmacology67 citations Open access
Semantic Scholar
Can SARS-CoV-2 Accumulate Mutations in the S-Protein to Increase Pathogenicity?
A. Padhi, Timir Tripathi
2020ACS Pharmacology & Translational Science67 citations Open access
Semantic Scholar
Scanning the RBD-ACE2 molecular interactions in Omicron variant
S. Rath, A. Padhi, N. Mandal
2021bioRxiv57 citations Open access
Semantic Scholar
Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis
A. Padhi, H. Kumar, S. Vasaikar, B. Jayaram +1 more
2012PLoS ONE53 citations Open access
Semantic Scholar
Accelerating COVID-19 Research Using Molecular Dynamics Simulation.
A. Padhi, S. Rath, Timir Tripathi
2021Journal of Physical Chemistry B52 citations
Semantic Scholar
Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations
A. Padhi, B. Jayaram, J. Gomes
2013Scientific Reports50 citations Open access
Semantic Scholar
A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS
Motoi Yamashita, H. Kuehn, K. Okuyama, S. Okada +16 more
2021Nature Immunology48 citations Open access
Semantic Scholar
The VP4 Peptide of Hepatitis A Virus Ruptures Membranes through Formation of Discrete Pores
Ashutosh Shukla, A. Padhi, J. Gomes, Manidipa Banerjee
2014Journal of Virology40 citations Open access
Semantic Scholar
Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Sota Yagi, A. Padhi, J. Vucinic, S. Barbe +5 more
2021Journal of the American Chemical Society39 citations
Semantic Scholar
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks
S. Vasaikar, A. Padhi, B. Jayaram, J. Gomes
2013BMC Neuroscience33 citations Open access
Semantic Scholar
Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes
A. Padhi, Timir Tripathi
2022bioRxiv32 citations Open access
Semantic Scholar
Molecular dynamics simulations: Principles, methods, and applications in protein conformational dynamics
A. Padhi, Matej Janezic, Kam Y. J. Zhang
2022Advances in Protein Molecular and Structural Biology Methods32 citations
Semantic Scholar
Identification and characterization of novel and rare susceptible variants in Indian amyotrophic lateral sclerosis patients
Priyam Narain, A. Padhi, Upma Dave, Dibyakanti Mishra +3 more
2019Neurogenetics28 citations
Semantic Scholar
Interface‐based design of the favipiravir‐binding site in SARS‐CoV‐2 RNA‐dependent RNA polymerase reveals mutations conferring resistance to chain termination
A. Padhi, J. Dandapat, Prakash Saudagar, V. Uversky +1 more
2021FEBS Letters27 citations Open access
Semantic Scholar
Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern
N. Mandal, A. Padhi, S. Rath
2022bioRxiv26 citations Open access
Semantic Scholar
Targeted design of drug binding sites in the main protease of SARS-CoV-2 reveals potential signatures of adaptation
A. Padhi, Timir Tripathi
2021Biochemical and Biophysical Research Communications - BBRC26 citations Open access
Semantic Scholar
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens.
A. Padhi, Timir Tripathi
2022Briefings in Functional Genomics18 citations
Semantic Scholar
Computational Protein Design for COVID-19 Research and Emerging Therapeutics
P. Kalita, Timir Tripathi, A. Padhi
2023ACS Central Science16 citations Open access
Semantic Scholar
Fast prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis
A. Padhi, S. Vasaikar, B. Jayaram, J. Gomes
2013FEBS Letters16 citations Open access
Semantic Scholar
Designing a vaccine for fascioliasis using immunogenic 24 kDa mu-class glutathione s-transferase.
Jupitara Kalita, A. Padhi, Timir Tripathi
2020Infection, Genetics and Evolution15 citations
Semantic Scholar
Computational and Functional Characterization of Angiogenin Mutations, and Correlation with Amyotrophic Lateral Sclerosis
A. Padhi, Kamalika Banerjee, J. Gomes, Manidipa Banerjee
2014PLoS ONE15 citations Open access
Semantic Scholar
Angiogenin mutations in Hungarian patients with amyotrophic lateral sclerosis: Clinical, genetic, computational, and functional analyses
Kornelia Tripolszki, J. Danis, A. Padhi, J. Gomes +6 more
2019Brain and Behavior13 citations Open access
Semantic Scholar
Insights into the role of d‐amino acid oxidase mutations in amyotrophic lateral sclerosis
A. Padhi, Saugata Hazra
2018Journal of Cellular Biochemistry13 citations
Semantic Scholar
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes
A. Padhi, Ashutosh Kumar, Ken-ichi Haruna, Haruna Sato +8 more
2021Briefings Bioinform.12 citations
Semantic Scholar
High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19
A. Padhi, P. Kalita, Kam Y. J. Zhang, Timir Tripathi
2020bioRxiv12 citations Open access
Semantic Scholar
A molecular dynamics based investigation reveals the role of rare Ribonuclease 4 variants in amyotrophic lateral sclerosis susceptibility.
A. Padhi, J. Gomes
2019Mutation research12 citations
Semantic Scholar
Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis
A. Padhi, Kam Y. J. Zhang
2020Scientific Reports11 citations Open access
Semantic Scholar
Insights into the role of ribonuclease 4 polymorphisms in amyotrophic lateral sclerosis
A. Padhi, Priyam Narain, Upma Dave, Rohit Satija +2 more
2019Journal of Biomolecular Structure and Dynamics11 citations
Semantic Scholar
Understanding the molecular interactions of inhibitors against Bla1 beta-lactamase towards unraveling the mechanism of antimicrobial resistance.
Sourya Bhattacharya, A. Padhi, V. Junghare, Neeladrisingha Das +4 more
2021International Journal of Biological Macromolecules10 citations
Semantic Scholar
High-throughput design of symmetrical dimeric SARS-CoV-2 main protease: structural and physical insights into hotspots for adaptation and therapeutics.
A. Padhi, Timir Tripathi
2022Physical Chemistry, Chemical Physics - PCCP9 citations
Semantic Scholar
Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance
A. Padhi, Rohit Shukla, Timir Tripathi
2020bioRxiv9 citations Open access
Semantic Scholar
Rare Angiogenin and Ribonuclease 4 variants associated with amyotrophic lateral sclerosis exhibit loss-of-function: a comprehensive in silico study
A. Padhi, Priyam Narain, J. Gomes
2019Metabolic brain disease9 citations
Semantic Scholar
Geranyl Diphosphate Synthase (CrtE) Inhibition Using Alendronate Enhances Isoprene Production in Recombinant Synechococcus elongatus UTEX 2973: A Step towards Isoprene Biorefinery
Indrajeet Yadav, Akhil Rautela, Agendra Gangwar, V. Kesari +2 more
2023Fermentation8 citations Open access
Semantic Scholar
How Does Arbidol Inhibit the Novel Coronavirus SARS-CoV-2? Atomistic Insights from Molecular Dynamics Simulations
A. Padhi, Aniruddha Seal, Timir Tripathi
20208 citations Open access
Semantic Scholar
Impaired tissue homing by the Ikzf3N159S variant is mediated by interfering with Ikaros function
J. Chang, Motoi Yamashita, A. Padhi, Kam Y. J. Zhang +1 more
2023Frontiers in Immunology6 citations Open access
Semantic Scholar
Comprehensive analysis of liquid–liquid phase separation propensities of HSV‐1 proteins and their interaction with host factors
Sushma Subedi, Niharika Nag, Harish Shukla, A. Padhi +1 more
2023Journal of Cellular Biochemistry6 citations
Semantic Scholar
From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics.
A. Padhi, P. Kalita, Shweata Maurya, Krishna Mohan Poluri +1 more
2023Journal of Physical Chemistry B6 citations
Semantic Scholar
Interface‐Guided Computational Protein Design Reveals Bebtelovimab‐Resistance Mutations in SARS‐CoV‐2 RBD: Correlation with Global Viral Genomes and Bebtelovimab‐Escape Mutations
Shweata Maurya, Shivank Kumar, A. Padhi
2023ChemistrySelect5 citations
Semantic Scholar
Multi-pathogen based chimeric vaccine to fight against COVID-19 and concomitant coinfections
Rupal Ojha, Satyendra Singh, Nidhi Gupta, K. Kumar +2 more
2023Biotechnology Letters5 citations Open access
Semantic Scholar
A distant angiogenin variant causes amyotrophic lateral sclerosis through loss-of-function mechanisms: Insights from long-timescale atomistic simulations and conformational dynamics
A. Padhi, Rohit Shukla, Priyam Narain, J. Gomes
2021Comput. Biol. Medicine5 citations
Semantic Scholar
Previously titled : ANGDelMut – a web-based tool for predicting and analyzing functional loss mechanisms of deleterious angiogenin mutations causing amyotrophic lateral sclerosis
A. Padhi, S. Vasaikar, B. Jayaram, J. Gomes
20145 citations
Semantic Scholar
Immunoinformatics Protocol to Design Multi-Epitope Subunit Vaccines.
P. Kalita, A. Padhi, Timir Tripathi
2023Methods in molecular biology3 citations
Semantic Scholar
Delineating the Structure–Dynamics–Binding Differences among BA.1, BA.4/5, and BF.7 SARS-CoV-2 Variants through Atomistic Simulations: Correlation with Structural and Epidemiological Features
Aryaman Joshi, Shweata Maurya, Atharva Mahale, S. Rath +2 more
2023ACS Omega3 citations Open access
Semantic Scholar
Corrigendum to “Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2” [Microbial Pathog. 145 (2020) 104236]
P. Kalita, A. Padhi, Kam Y. J. Zhang, Timir Tripathi
2020Microbial Pathogenesis3 citations Open access
Semantic Scholar
ANGDelMut – a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations
A. Padhi, S. Vasaikar, B. Jayaram, J. Gomes
2013F1000Research3 citations Open access
Semantic Scholar
Functional expression, localization, and biochemical characterization of thioredoxin glutathione reductase from air-breathing magur catfish, Clarias magur.
Debaprasad Koner, Niharika Nag, P. Kalita, A. Padhi +2 more
2023International Journal of Biological Macromolecules2 citations
Semantic Scholar
Computational Approaches for Development of Engineered Therapeutics against SARS-CoV-2
Aryaman Joshi, Timir Tripathi, S. Singh, A. Padhi
2022Biochemistry2 citations
Semantic Scholar

Frequent co-authors

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Timir Tripathi×23
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Timir Tripathi — researcher profile on SciRah
J. Gomes×14
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J. Gomes — researcher profile on SciRah
Kam Y. J. Zhang×10
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Kam Y. J. Zhang — researcher profile on SciRah
P. Kalita×8
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P. Kalita — researcher profile on SciRah

×6

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B. Jayaram — researcher profile on SciRah

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S. Vasaikar — researcher profile on SciRah

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Priyam Narain×4

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Rohit Shukla×3

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Shweata Maurya×3

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Harish Shukla×2

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Harish Shukla — researcher profile on SciRah

Prakash Saudagar×2

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Prakash Saudagar — researcher profile on SciRah