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  1. No Access

    Protocol

    Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses

    The conventional drug discovery pipeline involving discovery of a new molecule requires huge investment and long time. Therefore, re-using the existing drugs for new indication which is termed as “drug repurpo...

    Sohini Chakraborti,Sneha Bheemireddy,Narayanaswamy Srinivasan(2021)

  2. No Access

    Chapter

    Protein Structure, Dynamics and Assembly: Implications for Drug Discovery

    Most of the therapeutic drugs available in the market today, are targeted against proteins. Drug molecules are designed to complement shape, size and electrostatic fingerprints of the functional site of a targ...

    Arangasamy Yazhini,Sohini ChakrabortiinInnovations and Implementations of Compute…(2021)

  3. Article

    Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

    Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a c...

    Arindam Maitra,Mamta Chawla Sarkar,Harsha RahejainJournal of Biosciences(2020)

  4. Article

    Open Access

    iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

    Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure...

    Guilhem Faure,Agnel Praveen JosephinSource Code for Biology and Medicine(2019)

  5. Article

    Open Access

    Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions

    Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of resid...

    Srinivasan Jayashree,Pavalam Murugavel,Ramanathan SowdhaminiinBiology Direct(2019)

  6. No Access

    Protocol

    Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest

    Drug repurposing has garnered much interest as an effective method for drug development among biopharmaceutical companies. The availability of information on complete sequences of genomes and their associated ...

    Sohini Chakraborti,Gayatri RamakrishnaninComputational Methods for Drug Repurposing(2019)

  7. Article

    Open Access

    Use of designed sequences in protein structure recognition

    Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein s...

    Gayatri Kumar,Richa Mudgal,Narayanaswamy Srinivasan,Sankaran SandhyainBiology Direct(2018)

  8. Article

    Open Access

    Exploring anti-malarial potential of FDA approved drugs: an in silico approach

    The critically important issue on emergence of drug-resistant malarial parasites is compounded by cross resistance, where resistance to one drug confers resistance to other chemically similar drugs or those th...

    Gayatri Ramakrishnan,Nagasuma Chandra,Narayanaswamy SrinivasaninMalaria Journal(2017)

  9. Article

    Open Access

    Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins

    The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for...

    Ramachandran Rakesh,Rangachari Krishnan,伊芙琳SattleggerinBiology Direct(2017)

  10. Article

    Open Access

    Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria

    Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...

    Gayatri Ramakrishnan,Abha Jain,Nagasuma ChandrainBiology Direct(2016)

  11. No Access

    Protocol

    Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues

    With the advent of genome sequencing projects in the recent past, several kinases have come to light as regulating different signaling pathways. These kinases are generally classified into different subfamilie...

    Chintalapati JanakiinData Mining Techniques for the Life Scienc…(2016)

  12. No Access

    Protocol

    Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins

    Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpre...

    Ramachandran RakeshinData Mining Techniques for the Life Scienc…(2016)

  13. Article

    Open Access

    De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

    In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...

    Richa Mudgal,Sankaran Sandhya,Nagasuma ChandrainBiology Direct(2015)

  14. Article

    Open Access

    CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

    The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can...

    Mutharasu Gnanavel,Prachi Mehrotra,Ramaswamy RakshambikaiinBMC Bioinformatics(2014)

  15. No Access

    Protocol

    Recognition of Nontrivial Remote Homology Relationships Involving Proteins ofHelicobacter pylori: Implications for Function Recognition

    This chapter explains techniques for recognition of nontrivial remote homology relationships involving proteins ofHelicobacter pyloriand their implications for function recognition. Using the remote homology de...

    Nidhi Tyagi,Narayanaswamy SrinivasaninIn Silico Models for Drug Discovery(2013)

  16. Article

    Open Access

    The origins of the evolutionary signal used to predict protein-protein interactions

    The correlation of genetic distances between pairs of protein sequence alignments has been used to infer protein-protein interactions. It has been suggested that these correlations are based on the signal of c...

    Lakshmipuram S Swapna,Narayanaswamy SrinivasaninBMC Evolutionary Biology(2012)

  17. Article

    Open Access

    Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR

    交互的非结构蛋白5 a (NS5A)Hepatitis C virus (HCV) with human kinases namely, casein kinase 1α (ck1α) and protein kinase R (PKR) have different functional implications such as regulatio...

    Govindarajan Sudha,Subburaj Yamunadevi,Nidhi TyagiinBMC Structural Biology(2012)

  18. No Access

    Article

    Cistranspeptide variations in structurally similar proteins

    The presence of energetically less favourablecispeptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between thecisandtrans...

    Agnel Praveen Joseph,Narayanaswamy Srinivasan,Alexandre G. de BreverninAmino Acids(2012)

  19. Article

    Open Access

    Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

    Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stabl...

    Lakshmipuram S Swapna,Swapnil Mahajan,Alexandre G de BreverninBMC Structural Biology(2012)

  20. Article

    Open Access

    AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

    Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, A...

    Oruganty Krishnadev,Narayanaswamy SrinivasaninBMC Bioinformatics(2011)

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