Narayanaswamy Srinivasan

Summary

Country: India

Publications

  1. doi request reprint A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases
    Raju Kalaivani
    Molecular Biophysics Unit, Indian Institute of Science, Lab no 103, Bangalore 560012, Karnataka, India
    Mol Biosyst 11:1079-95. 2015
  2. pmc CLAP: a web-server for automatic classification of proteins with special reference to multi-domain proteins
    Mutharasu Gnanavel
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    BMC Bioinformatics 15:343. 2014
  3. pmc Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
    R Bhadra
    Molecular Biophysics Unit, Indian Institute of Science, 560 012, Bangalore, India
    Nucleic Acids Res 34:W143-6. 2006
  4. pmc PIC: Protein Interactions Calculator
    K G Tina
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 35:W473-6. 2007
  5. pmc MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
    V S Gowri
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Nucleic Acids Res 34:D243-6. 2006
  6. pmc PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
    O Krishnadev
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 33:W126-9. 2005
  7. pmc DoSA: Database of Structural Alignments
    Swapnil Mahajan
    Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR S INSERM S665, Faculté des Sciences et Technologies, Universite de la Reunion, F 97715 Saint Denis Messag Cedex 09, La Reunion, France
    Database (Oxford) 2013:bat048. 2013
  8. pmc Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes
    R Rakshambikai
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Comp Funct Genomics 2012:258284. 2012
  9. doi request reprint Tethering preferences of domain families co-occurring in multi-domain proteins
    Smita Mohanty
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Mol Biosyst 9:1708-25. 2013
  10. pmc Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
    Lakshmipuram S Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    BMC Struct Biol 12:6. 2012

Collaborators

Detail Information

Publications108 found, 100 shown here

  1. doi request reprint A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases
    Raju Kalaivani
    Molecular Biophysics Unit, Indian Institute of Science, Lab no 103, Bangalore 560012, Karnataka, India
    Mol Biosyst 11:1079-95. 2015
    ..Finally, we show that the perceived fluctuations serve as a useful input to predict the functional state of a kinase. ..
  2. pmc CLAP: a web-server for automatic classification of proteins with special reference to multi-domain proteins
    Mutharasu Gnanavel
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    BMC Bioinformatics 15:343. 2014
    ..Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better...
  3. pmc Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
    R Bhadra
    Molecular Biophysics Unit, Indian Institute of Science, 560 012, Bangalore, India
    Nucleic Acids Res 34:W143-6. 2006
    ..We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html...
  4. pmc PIC: Protein Interactions Calculator
    K G Tina
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 35:W473-6. 2007
    ..User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside...
  5. pmc MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
    V S Gowri
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Nucleic Acids Res 34:D243-6. 2006
    ..An analysis interface allows display and convenient navigation of alignments and domain hits. MulPSSM can be accessed at http://crick.mbu.iisc.ernet.in/~mulpssm...
  6. pmc PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
    O Krishnadev
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 33:W126-9. 2005
    ..The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is http://hodgkin.mbu.iisc.ernet.in/~prodoc...
  7. pmc DoSA: Database of Structural Alignments
    Swapnil Mahajan
    Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR S INSERM S665, Faculté des Sciences et Technologies, Universite de la Reunion, F 97715 Saint Denis Messag Cedex 09, La Reunion, France
    Database (Oxford) 2013:bat048. 2013
    ..Database URL: http://bo-protscience.fr/dosa/..
  8. pmc Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes
    R Rakshambikai
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Comp Funct Genomics 2012:258284. 2012
    ..Overall the fugu serves as a good model organism to understand roles of human kinases as far as kinases such as LRRK and IRAK and their associated pathways are concerned...
  9. doi request reprint Tethering preferences of domain families co-occurring in multi-domain proteins
    Smita Mohanty
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Mol Biosyst 9:1708-25. 2013
    ..Thus, the analysis uncovers how domain families recombine and evolve to give rise to multi-domain proteins...
  10. pmc Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
    Lakshmipuram S Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    BMC Struct Biol 12:6. 2012
    ..In this work, we have addressed the question "What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?"..
  11. pmc The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations
    A Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Genome Biol 3:RESEARCH0066. 2002
    ....
  12. pmc Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families
    Ratna R Thangudu
    Laboratoire de Biochimie et Genetique Moleculaire, Universite de la Reunion, BP 7151, 15 Avenue Rene Cassin, 97715 Saint Denis Messag Cedex 09, La Reunion, France
    BMC Struct Biol 8:55. 2008
    ..We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue...
  13. pmc CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations
    Sankaran Sandhya
    National Centre for Biological Sciences TIFR, UAS GKVK Campus, Bellary Road, Bangalore 560 065, India
    BMC Struct Biol 8:28. 2008
    ..Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains...
  14. pmc Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different
    Subhajyoti De
    Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721 302, India
    BMC Struct Biol 5:15. 2005
    ..The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces...
  15. pmc Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions
    Nambudiry Rekha
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    BMC Struct Biol 3:4. 2003
    ..The tetramer cannot phosphorylate some substrates that can be phosphorylated by PKCK2alpha in isolation. The present work explores the structural basis of this feature using computational analysis and modeling...
  16. pmc Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes
    A Krupa
    Indian Institute of Science, Bangalore 560 012, India
    BMC Genomics 6:129. 2005
    ..The organisation of domains in a large dataset of bacterial STYKs has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial STYKs...
  17. pmc SUPFAM: a database of sequence superfamilies of protein domains
    Shashi B Pandit
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    BMC Bioinformatics 5:28. 2004
    ..Subsequently all-against-all family profile matches are made to deduce a list of new potential superfamilies of yet unknown structure...
  18. ncbi request reprint Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues
    B Anand
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Bioinformatics 21:2821-6. 2005
    ..In this work we demonstrate that the use of multiple PSSMs corresponding to a given alignment and variable reference sequences is more effective than using traditional single PSSMs and hidden Markov models...
  19. pmc A framework for classification of prokaryotic protein kinases
    Nidhi Tyagi
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 5:e10608. 2010
    ..A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases...
  20. ncbi request reprint Structural interpretation of site-directed mutagenesis and specificity of the catalytic subunit of protein kinase CK2 using comparative modelling
    N Srinivasan
    Department of Biochemistry, University of Cambridge, UK
    Protein Eng 12:119-27. 1999
    ....
  21. ncbi request reprint Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures
    Seema Namboori
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    In Silico Biol 4:445-60. 2004
    ..Importantly, the public availability of these profiles from us could enable one to perform genome wide structure assignment in a local machine in a fast and accurate manner...
  22. pmc Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations
    Krishanpal Anamika
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    BMC Genomics 9:625. 2008
    ..Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human...
  23. pmc Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold
    Garima Agarwal
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 4:e5736. 2009
    ..We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function...
  24. pmc Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR
    Govindarajan Sudha
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
    BMC Struct Biol 12:28. 2012
    ..Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV...
  25. ncbi request reprint A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
    Manoj Tyagi
    Laboratoire de Biochimie et Genetique Moleculaire, Universite de la Reunion, BP 7151, 15 Avenue Rene Cassin, 97715 Saint Denis Messag Cedex 09, La Reunion, France
    Proteins 65:32-9. 2006
    ..Lastly, using protein kinase as an example, we identify regions of conformational variations and rigid body movements in the enzyme as it is changed to the active state from an inactive state...
  26. pmc Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage
    Swati Kaushik
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
    PLoS ONE 8:e56449. 2013
    ..thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST...
  27. ncbi request reprint A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite
    Oruganty Krishnadev
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    In Silico Biol 8:235-50. 2008
    ..The method described is generally applicable to any host-pathogen pair and can thus be of general value to studies of host-pathogen protein-protein interactions...
  28. doi request reprint Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins
    Ramachandra M Bhaskara
    a Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    J Biomol Struct Dyn 31:1467-80. 2013
    ..Results of our analysis provide guidelines in modelling of multi-domain proteins from the tertiary structures of constituent domain components. ..
  29. ncbi request reprint Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv
    Seema Namboori
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012
    J Biosci 29:245-59. 2004
    ..MTB-specific proteins might include factors responsible for virulence. Importantly, these assignments could be valuable for experimental endeavors. The detailed results are publicly available at http://hodgkin.mbu.iisc.ernet.in/~dots...
  30. doi request reprint Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability
    Richa Mudgal
    IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, India
    J Mol Biol 426:962-79. 2014
    ..Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. ..
  31. ncbi request reprint Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: implications for function annotation based on homology searches and structural genomics
    Ambrish Roy
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    In Silico Biol 9:S41-55. 2009
    ..Our work provides guidelines on the functional annotation based on homology searches and in structural genomics initiatives...
  32. pmc Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks
    Garima Agarwal
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 6:e17826. 2011
    ..This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure...
  33. doi request reprint The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins
    Ramachandra M Bhaskara
    Molecular Biophysics Unit, Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India
    Mol Biosyst 10:1082-93. 2014
    ..This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences. ..
  34. pmc Functional diversity of human protein kinase splice variants marks significant expansion of human kinome
    Krishanpal Anamika
    Indian Institute of Science, Bangalore, India
    BMC Genomics 10:622. 2009
    ..However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants...
  35. doi request reprint Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies
    Agnel Praveen Joseph
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Biochimie 94:2025-34. 2012
    ..Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods...
  36. pmc iPBA: a tool for protein structure comparison using sequence alignment strategies
    Jean Christophe Gelly
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Nucleic Acids Res 39:W18-23. 2011
    ..As a fast and efficient 'sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/...
  37. pmc Cis-trans peptide variations in structurally similar proteins
    Agnel Praveen Joseph
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Denis Diderot Paris 7, INTS, 6 rue Alexandre Cabanel, Paris Cedex 15, France
    Amino Acids 43:1369-81. 2012
    ..Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution...
  38. pmc The origins of the evolutionary signal used to predict protein-protein interactions
    Lakshmipuram S Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    BMC Evol Biol 12:238. 2012
    ..However, it has been argued that the correlated rates of evolution used to predict protein interaction explicitly includes shared evolutionary history; here we test this hypothesis...
  39. pmc Protein-protein interactions in clathrin vesicular assembly: radial distribution of evolutionary constraints in interfaces
    Rupali A Gadkari
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 7:e31445. 2012
    ..This points to the strategy adopted by the nature to package diverse proteins but transport them through a highly conserved mechanism...
  40. doi request reprint Prediction of protein-protein interactions between Helicobacter pylori and a human host
    Nidhi Tyagi
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Mol Biosyst 5:1630-5. 2009
    ..Structural analysis of some of the examples reveals that the interaction predicted by us is consistent with the structural compatibility of binding partners. Examples of interactions with discernible biological relevance are discussed...
  41. ncbi request reprint Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins
    S Balaji
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Protein Eng 14:219-26. 2001
    ..The PALI database is expected to be useful in furthering our understanding of the relationship between sequences and structures of homologous proteins and their evolution...
  42. ncbi request reprint Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways
    N Rekha
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Proteins 58:339-53. 2005
    ..We discuss a few representative cases of diverging pathways involving domains in a superfamily...
  43. ncbi request reprint Mutational analysis of the Mycobacterium tuberculosis Rv1625c adenylyl cyclase: residues that confer nucleotide specificity contribute to dimerization
    Avinash R Shenoy
    Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
    FEBS Lett 545:253-9. 2003
    ....
  44. ncbi request reprint Assessment of a rigorous transitive profile based search method to detect remotely similar proteins
    S Sandhya
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    J Biomol Struct Dyn 23:283-98. 2005
    ..Such a propagation of searches maximizes the chances of detecting distant homologies by effectively scanning protein "fold space"...
  45. pmc Extent of structural asymmetry in homodimeric proteins: prevalence and relevance
    Lakshmipuram Seshadri Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 7:e36688. 2012
    ..Our study provides new insights regarding accommodation of asymmetry in homodimers...
  46. pmc Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum
    Smita Amarnath
    Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
    PLoS ONE 7:e30644. 2012
    ..We speculate that the existence of the second role can act as a safeguard against perturbations to ribosome function caused by spontaneous variations in DdS4 levels...
  47. pmc Classification of protein kinases on the basis of both kinase and non-kinase regions
    Juliette Martin
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 5:e12460. 2010
    ..Many protein kinases are multi-domain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies...
  48. doi request reprint Recognition of nontrivial remote homology relationships involving proteins of Helicobacter pylori: implications for function recognition
    Nidhi Tyagi
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Methods Mol Biol 993:155-75. 2013
    ..Further, homologues of enzymes that potentially catalyze step(s) in various metabolic processes in H. pylori have been identified for the first time...
  49. pmc AlignHUSH: alignment of HMMs using structure and hydrophobicity information
    Oruganty Krishnadev
    Molecular Biophysics Unit Indian Institute of Science, Bangalore 560012, India
    BMC Bioinformatics 12:275. 2011
    ..The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection...
  50. pmc Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures
    Rupali A Gadkari
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    BMC Struct Biol 10:17. 2010
    ..However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive...
  51. ncbi request reprint A new domain family in the superfamily of alkaline phosphatases
    Rana Bhadra
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    In Silico Biol 5:379-87. 2005
    ..Additionally, set of residues responsible for a metal binding site in phosphatases and sulphtases are conserved in the new family. The in-depth analysis suggests that the new family could possess phosphatase activity...
  52. pmc Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha) atoms
    Rupali A Gadkari
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 4:e4476. 2009
    ..Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha) atoms which are modeled with modest accuracy...
  53. pmc Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
    V S Gowri
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 31:486-8. 2003
    ..The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali...
  54. pmc SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
    Shashi B Pandit
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 30:289-93. 2002
    ..Fifty-one of these Pfam families of unknown structure could be clustered into 17 potentially new superfamilies forming good targets for structural genomics. SUPFAM database can be accessed at http://pauling.mbu.iisc.ernet.in/~supfam...
  55. doi request reprint The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function
    Prasanna Bhat
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 43:2888-901. 2015
    ..Taken together, results provide novel molecular insights into IRES-RPS5 interaction and unravel its functional significance in mediating internal initiation of translation. ..
  56. doi request reprint Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function
    Gayatri Ramakrishnan
    Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India Electronic address
    Tuberculosis (Edinb) 95:14-25. 2015
    ....
  57. pmc Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling
    Ramaswamy Rakshambikai
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 8:e78753. 2013
    ..The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation. ..
  58. pmc Stability of domain structures in multi-domain proteins
    Ramachandra M Bhaskara
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Sci Rep 1:40. 2011
    ..Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR...
  59. doi request reprint NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection
    Richa Mudgal
    IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, Karnataka, India
    Nucleic Acids Res 43:D300-5. 2015
    ..The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user...
  60. pmc Length variations amongst protein domain superfamilies and consequences on structure and function
    Sankaran Sandhya
    National Centre for Biological Sciences TIFR, GKVK Campus, Bangalore, India
    PLoS ONE 4:e4981. 2009
    ..Related protein domains of a superfamily can be specified by proteins of diverse lengths. The structural and functional implications of indels in a domain scaffold have been examined...
  61. doi request reprint Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure
    Swapnil Mahajan
    a Faculté des Sciences et Technologies, Universite de la Reunion, F 97715 Saint Denis Messag Cedex 09, La Reunion, France
    J Biomol Struct Dyn 32:751-8. 2014
    ....
  62. doi request reprint Novel insertion and deletion mutants of RpoB that render Mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription
    Vidyasagar Malshetty
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    Microbiology 156:1565-73. 2010
    ..We discuss possible uses of the RpoB mutants in studying transcriptional regulation in mycobacteria and as potential targets for drug design...
  63. ncbi request reprint A conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer
    Ananth Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Trends Biochem Sci 28:9-12. 2003
    ..We also identify remote similarity of this domain to the nucleotidyl transferases and, hence, this domain is suggested to be invloved in the adenylylation reaction of FAD synthetases...
  64. doi request reprint Evolution of domain combinations in protein kinases and its implications for functional diversity
    Krupa Deshmukh
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Prog Biophys Mol Biol 102:1-15. 2010
    ..Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization...
  65. ncbi request reprint Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures
    S Balaji
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Proteins 53:783-91. 2003
    ..These carbonyls and amides are usually located in the loops that are structurally variable among homologous proteins...
  66. ncbi request reprint Functional inactivation of the human guanylyl cyclase C receptor: modeling and mutation of the protein kinase-like domain
    R Bhandari
    Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
    Biochemistry 40:9196-206. 2001
    ....
  67. ncbi request reprint Stranded in isolation: structural role of isolated extended strands in proteins
    Narayanan Eswar
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Protein Eng 16:331-9. 2003
    ..It is suggested that isolated beta-strands have many characteristics of loop segments but with repetitive (phi,psi) values falling within the beta-region of the Ramachandran map...
  68. ncbi request reprint Identification and analysis of a new family of bacterial serine proteinases
    Shashi B Pandit
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    In Silico Biol 4:563-72. 2004
    ....
  69. ncbi request reprint Influence of solvent molecules on the stereochemical code of glycyl residues in proteins
    Narayanan Eswar
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Proteins 49:326-34. 2002
    ..It is suggested that water molecules play a key role in determining and stabilizing these conformations of glycyl residues and explain the aberration in the symmetry of glycyl conformations in proteins...
  70. ncbi request reprint Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution
    S Balaji
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    J Biosci 32:83-96. 2007
    ..Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low...
  71. ncbi request reprint Structural modes of stabilization of permissive phosphorylation sites in protein kinases: distinct strategies in Ser/Thr and Tyr kinases
    A Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    J Mol Biol 339:1025-39. 2004
    ..The comparison of their crystal structures and the distinct features observed are hoped to aid in the understanding of mechanisms underlying the control of the catalytic activity of distinct subgroups of protein kinases...
  72. ncbi request reprint Evolutionary divergence of Plasmodium falciparum: sequences, protein-protein interactions, pathways and processes
    Nidhi Tyagi
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Infect Disord Drug Targets 9:257-71. 2009
    ..We also discuss examples of protein-protein interactions across human and P. falciparum potentially happening during pathogenesis...
  73. ncbi request reprint Proteomics analysis of carbon-starved Mycobacterium smegmatis: induction of Dps-like protein
    Surbhi Gupta
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Protein Eng 15:503-12. 2002
    ..Using comparative modelling we were able to show that Dps from M.smegmatis could form a dodecamer structure similar to the crystal structure of Dps from Escherichia coli...
  74. pmc Hybrid and rogue kinases encoded in the genomes of model eukaryotes
    Ramaswamy Rakshambikai
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    PLoS ONE 9:e107956. 2014
    ..Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions. ..
  75. pmc Small molecule inhibitors of HCV replication from pomegranate
    B Uma Reddy
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    Sci Rep 4:5411. 2014
    ..Taken together, our study provides a proof-of-concept approach for the potential use of antiviral and non-toxic principle ellagitannins from pomegranate in prevention and control of HCV induced complications. ..
  76. pmc Functional characterization and structural modelling of late gene expression factor 4 from Bombyx mori nucleopolyhedrovirus
    Seema Sehrawat
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    Biochem J 368:159-69. 2002
    ....
  77. doi request reprint Importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the M1 family: Thermoplasma acidophilum Tricorn interacting factor F2 and Escherichia coli Peptidase N
    Anujith Kumar
    Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
    Biochimie 91:1145-55. 2009
    ..Together, these studies revealed that non-conserved distal C-terminal aa repress the surface exposure of apolar aa, enhance protein solubility, and catalytic activity in two soluble and distinct members of the M1 family...
  78. ncbi request reprint Effective detection of remote homologues by searching in sequence dataset of a protein domain fold
    S Sandhya
    Molecular Biophysics Unit, Indian Institute of Science, 560 012 Bangalore, India
    FEBS Lett 552:225-30. 2003
    ..We also discuss the implications of using this strategy to link sequence and structure space...
  79. ncbi request reprint Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases
    V S Gowri
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    J Biosci 32:921-8. 2007
    ..We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis...
  80. pmc Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases
    A Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Protein Sci 11:1580-4. 2002
    ..It has been suggested here that RIO1 proteins are intermediately related to lipopolysaccharide kinases and eukaryotic protein kinases implying an evolutionary relationship between the three classes of proteins...
  81. ncbi request reprint PALI: a database of alignments and phylogeny of homologous protein structures
    S Sujatha
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Bioinformatics 17:375-6. 2001
    ....
  82. ncbi request reprint Structural compromise of disallowed conformations in peptide and protein structures
    C Ramakrishnan
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Protein Pept Lett 14:672-82. 2007
    ....
  83. doi request reprint An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles
    Govindarajan Sudha
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India Electronic address
    Prog Biophys Mol Biol 116:141-50. 2014
    ..Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. ..
  84. pmc Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA
    Agnel Praveen Joseph
    Molecular Biophysics Unit Indian Institute of Science, Bangalore, India Present address Science and Technology Facilities Council, RAL, Harwell, Didcot, UK
    RNA Biol 11:891-905. 2014
    ....
  85. doi request reprint Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling
    Ramachandra M Bhaskara
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    Proteins 82:1219-34. 2014
    ..We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions...
  86. ncbi request reprint Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen
    Renuka Pudi
    Department of Microbiology and Cell Biology and the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    J Biol Chem 278:12231-40. 2003
    ..The results presented here strongly suggest that both the N- and C-terminal halves can interact independently with the HCV IRES and are involved in stimulating internal initiation of translation...
  87. pmc Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation
    Sunanda R Singh
    Department of Microbiology, Indian Institute of Science, Bangalore 12, India
    Nucleic Acids Res 32:201-10. 2004
    ..This study indicates a structural and functional conservation of different Rpb7 across species and also a conserved role of Rpb7 in the subcomplex with respect to nutritional stress...
  88. ncbi request reprint Analysis of the protein kinome of Entamoeba histolytica
    K Anamika
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Proteins 71:995-1006. 2008
    ..Our kinome analysis of E. histolytica suggests that the organism possesses a complex protein phosphorylation network that involves many unusual kinases...
  89. ncbi request reprint Interaction between two residues in the inter-domain interface of Escherichia coli peptidase N modulates catalytic activity
    Anujith Kumar
    Department of Biochemistry, Indian Institute of Science, Bangalore, India 560012
    Protein Pept Lett 16:415-22. 2009
    ..Structural analysis shows this interaction to change the relative disposition of active site residues, which modulates catalytic activity...
  90. pmc KinG: a database of protein kinases in genomes
    A Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Nucleic Acids Res 32:D153-5. 2004
    ..Another exclusive feature of the database is the collection of the Ser/Thr/Tyr protein kinases and similar sequences encoded in the genomes of archaea and bacteria...
  91. ncbi request reprint Strategies for the effective identification of remotely related sequences in multiple PSSM search approach
    V S Gowri
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    Proteins 67:789-94. 2007
    ....
  92. ncbi request reprint Genome-wide comparative analyses of domain organisation of repertoires of protein kinases of Arabidopsis thaliana and Oryza sativa
    A Krupa
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Gene 380:1-13. 2006
    ..Putative homologues of protein kinases of A. thaliana that regulate plant-specific physiological processes like ethylene hormone response, somatic embryogenesis and pathogen defence have been identified in O. sativa genome as well...
  93. ncbi request reprint The ascent of nucleotide cyclases: conservation and evolution of a theme
    Avinash R Shenoy
    Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
    J Biosci 27:85-91. 2002
  94. ncbi request reprint Identification of "missing" metabolic proteins of Plasmodium falciparum: a bioinformatics approach
    Smita Mohanty
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Protein Pept Lett 16:961-8. 2009
    ..In a few cases we also provide the list of functionally important residues extrapolated on the basis of homology...
  95. ncbi request reprint The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae
    Vinaya Sampath
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    J Biol Chem 278:51566-76. 2003
    ..Taken together, our results allow us to assign phenotype-specific roles for the different conserved and non-conserved regions of Rpb4...
  96. ncbi request reprint Survey for g-proteins in the prokaryotic genomes: prediction of functional roles based on classification
    Shashi B Pandit
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Proteins 52:585-97. 2003
    ..The large GTP-binding proteins and the alpha-subunit of heterotrimeric G-proteins are not detected in the genomes of the prokaryotes surveyed...