Shandar Ahmad

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi request reprint Real value prediction of solvent accessibility from amino acid sequence
    Shandar Ahmad
    RIKEN Tsukuba Institute, Ibaraki, Japan
    Proteins 50:629-35. 2003
  2. pmc CCRXP: exploring clusters of conserved residues in protein structures
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8, Saito Asagi, Ibaraki, Osaka 5670085, Japan
    Nucleic Acids Res 38:W398-401. 2010
  3. pmc Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
    Mizuki Morita
    Department of Fundamental Research, National Institute of Biomedical Innovation, 7 6 8 Saito Asagi, Ibaraki, Osaka, Japan
    BMC Biophys 4:21. 2011
  4. pmc Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8, Saito Asagi, Ibaraki, Osaka 567 0085, Graduate School of Frontier Biosciences, Osaka University, Japan
    Nucleic Acids Res 36:5922-32. 2008
  5. pmc Integrated pathway clusters with coherent biological themes for target prioritisation
    Yi an Chen
    National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
    PLoS ONE 9:e99030. 2014
  6. pmc Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8 Saito Asagi, Ibaraki, Osaka 567 0085, Japan
    BMC Bioinformatics 11:533. 2010
  7. ncbi request reprint Atom-wise statistics and prediction of solvent accessibility in proteins
    Y Hemajit Singh
    Department of Biosciences, Jamia Millia Islamia University, New Delhi 110025, India
    Biophys Chem 124:145-54. 2006
  8. ncbi request reprint Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression
    Jung Ying Wang
    Department of Computer Science and Information Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
    Proteins 61:481-91. 2005
  9. ncbi request reprint Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability
    Mohd Firdaus Raih
    National Institute for Genomics and Molecular Biology Interim Laboratory, and School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
    Biophys Chem 114:63-9. 2005
  10. ncbi request reprint SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine
    Jung Ying Wang
    Department of Computer Science and Information Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
    Proteins 68:82-91. 2007

Collaborators

Detail Information

Publications27

  1. ncbi request reprint Real value prediction of solvent accessibility from amino acid sequence
    Shandar Ahmad
    RIKEN Tsukuba Institute, Ibaraki, Japan
    Proteins 50:629-35. 2003
    ..Prediction error for each residue type strongly correlates with the variability in its experimental ASA values...
  2. pmc CCRXP: exploring clusters of conserved residues in protein structures
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8, Saito Asagi, Ibaraki, Osaka 5670085, Japan
    Nucleic Acids Res 38:W398-401. 2010
    ..We expect that CCRXP web server will be useful in studies of protein structures and their interactions and selecting mutagenesis targets. The web server can be accessed at http://ccrxp.netasa.org...
  3. pmc Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
    Mizuki Morita
    Department of Fundamental Research, National Institute of Biomedical Innovation, 7 6 8 Saito Asagi, Ibaraki, Osaka, Japan
    BMC Biophys 4:21. 2011
    ..abstract:..
  4. pmc Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8, Saito Asagi, Ibaraki, Osaka 567 0085, Graduate School of Frontier Biosciences, Osaka University, Japan
    Nucleic Acids Res 36:5922-32. 2008
    ..Overall, the conservation patterns of the stabilizing residues in DNA-binding proteins also highlight the significance of clustering as compared to single residue conservation...
  5. pmc Integrated pathway clusters with coherent biological themes for target prioritisation
    Yi an Chen
    National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
    PLoS ONE 9:e99030. 2014
    ....
  6. pmc Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins
    Shandar Ahmad
    National Institute of Biomedical Innovation, 7 6 8 Saito Asagi, Ibaraki, Osaka 567 0085, Japan
    BMC Bioinformatics 11:533. 2010
    ..These conformational changes often occur via residues that are inherently flexible and hence, predicting fluctuations in residue positions is of great significance...
  7. ncbi request reprint Atom-wise statistics and prediction of solvent accessibility in proteins
    Y Hemajit Singh
    Department of Biosciences, Jamia Millia Islamia University, New Delhi 110025, India
    Biophys Chem 124:145-54. 2006
    ..e., at an atomic level is expected to help in bioinformatics approaches to structure prediction, functional relevance of atomic solvent accessibilities and other interaction analyses...
  8. ncbi request reprint Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression
    Jung Ying Wang
    Department of Computer Science and Information Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
    Proteins 61:481-91. 2005
    ..Longer protein chains have been found to be more accurately predicted than their smaller counterparts...
  9. ncbi request reprint Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability
    Mohd Firdaus Raih
    National Institute for Genomics and Molecular Biology Interim Laboratory, and School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
    Biophys Chem 114:63-9. 2005
    ..This analysis and prediction results have significant implications towards determining interacting residues in proteins and for the prediction of protein-protein, protein-ligand, protein-DNA and similar interactions...
  10. ncbi request reprint SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine
    Jung Ying Wang
    Department of Computer Science and Information Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
    Proteins 68:82-91. 2007
    ..66. Since, the method starts with the prediction of discrete states of ASA and leads to real value predictions, performance of prediction in binary states and real values are simultaneously optimized...
  11. ncbi request reprint Dimensionality of amino acid space and solvent accessibility prediction with neural networks
    Marcos J Arauzo-Bravo
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka ken 820 8502, Japan
    Comput Biol Chem 30:160-8. 2006
    ..The method developed to find the optimal codification is general, although the codification thus produced is dependent on the type of estimated property...
  12. ncbi request reprint RVP-net: online prediction of real valued accessible surface area of proteins from single sequences
    Shandar Ahmad
    Department of Biochemical Engineering and Science, Kyushu Institute of Technology, IZUKA, 820 8502, Fukuoka Ken, Japan and Computational Biology Research Center CBRC, AIST, 2 41 6, Koto ku, Tokyo 135 0064, Japan
    Bioinformatics 19:1849-51. 2003
    ..To facilitate batch processing of several sequences, a standalone version of this tool is also provided...
  13. ncbi request reprint Design and training of a neural network for predicting the solvent accessibility of proteins
    Shandar Ahmad
    Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka Ken, Japan
    J Comput Chem 24:1313-20. 2003
    ..It has been established that the prediction accuracy results with neural network are better than other reported results of ASA prediction, despite a high test to training data ratio...
  14. doi request reprint A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea)
    Ritu Singh
    Department of Biosciences, Jamia Millia Islamia, New Delhi 110 025, India
    Biophys Chem 133:81-9. 2008
    ..DeltaC(p)(D) of the protein is also compared with that estimated using the known heat capacities of amino acid residues and their fractional area exposed on denaturation...
  15. pmc Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network
    Adeel Malik
    Department of Biosciences, Jamia Millia Islamia University, New Delhi 110025, India
    BMC Struct Biol 7:1. 2007
    ..A comparison of protein-carbohydrate complexes has also been made with other protein-ligand complexes...
  16. doi request reprint A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen
    Adeel Malik
    Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
    Int J Biol Macromol 42:185-90. 2008
    ..The structural and functional features of Hev b 4 could prove useful to elucidate its exposed epitopes which are important for IgE binding...
  17. ncbi request reprint Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition
    Marcos J Arauzo-Bravo
    Department of Biosciences and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820 8502, Japan
    J Am Chem Soc 127:16074-89. 2005
    ..This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands...
  18. ncbi request reprint Role of non-covalent interactions for determining the folding rate of two-state proteins
    M Michael Gromiha
    Computational Biology Research Center CBRC, National Institute of Advanced Industrial Science and Technology AIST, Aomi Frontier Building 17F, 2 43 Aomi, Koto ku, Tokyo 135 0064, Japan
    Biophys Chem 107:263-72. 2004
    ..Further, the combination of free energies with topological parameters yielded the correlation of 0.91. The present study demonstrates the importance of topology for determining the folding rate of two-state proteins...
  19. ncbi request reprint Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    Shandar Ahmad
    Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Fukuoka, Iizuka 820 8502, Japan
    Bioinformatics 20:477-86. 2004
    ..Using non-redundant databases of transcription factors and protein-DNA complexes, neural network models were developed to utilize the information present in this relationship to predict DNA-binding proteins and their binding residues...
  20. pmc ASAView: database and tool for solvent accessibility representation in proteins
    Shandar Ahmad
    Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka Ken, Japan
    BMC Bioinformatics 5:51. 2004
    ..Therefore, a method to quickly see the surface residues in a two dimensional model would help to immediately understand the population of amino acid residues on the surface and in the inner core of the proteins...
  21. pmc Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins
    Shandar Ahmad
    Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka Ken, Japan
    Nucleic Acids Res 32:W104-7. 2004
    ..We propose that such a tree representation will be helpful in detecting protein-protein interfaces, structure similarity and motif detection...
  22. ncbi request reprint Structural analysis of cation-pi interactions in DNA binding proteins
    M Michael Gromiha
    Computational Biology Research Center CBRC, National Institute of Advanced Industrial Science and Technology AIST, Aomi Frontier Building 17F, 2 43 Aomi, Koto ku, Tokyo 135 0064, Japan
    Int J Biol Macromol 34:203-11. 2004
    ..The results obtained in the present study will be useful in understanding the contribution of cation-pi interactions to the stability and specificity of protein-DNA complexes...
  23. ncbi request reprint Moment-based prediction of DNA-binding proteins
    Shandar Ahmad
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 4 Kawazu, Iizuka 820 8502, Fukuoka, Japan
    J Mol Biol 341:65-71. 2004
    ..The speed and accuracy of this method, in combination with homology-based methods of structure prediction, should enhance genome-wide recognition of DNA-binding proteins...
  24. ncbi request reprint Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis
    Jung Ying Wang
    Department of Multimedia and Game Science, Lunghwa University of Science and Technology, Taoyuan, Taiwan
    Biopolymers 75:209-16. 2004
    ..As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look-up tables are provided on the web at www.netasa.org/look-up/...
  25. pmc PSSM-based prediction of DNA binding sites in proteins
    Shandar Ahmad
    Department of Bioinformatics and Bioscience, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka, Japan
    BMC Bioinformatics 6:33. 2005
    ..Here we implement a neural network based algorithm to utilize evolutionary information of amino acid sequences in terms of their position specific scoring matrices (PSSMs) for a better prediction of DNA-binding sites...
  26. pmc TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins
    M Michael Gromiha
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, AIST Tokyo Waterfront Bio IT Research Building, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 33:W164-7. 2005
    ..The prediction server is available at http://psfs.cbrc.jp/tmbeta-net/...
  27. ncbi request reprint NETASA: neural network based prediction of solvent accessibility
    Shandar Ahmad
    Institute of Multimedia and Software, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
    Bioinformatics 18:819-24. 2002
    ..Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction...