Daniel Fischer

Summary

Affiliation: University at Buffalo
Country: USA

Publications

  1. pmc On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
    Yanbin Yin
    Computer Science and Engineering Dept 201 Bell Hall, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Evol Biol 6:63. 2006
  2. ncbi request reprint Servers for protein structure prediction
    Daniel Fischer
    Buffalo Center of Excellence in Bioinformatics, and Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY 14260, USA
    Curr Opin Struct Biol 16:178-82. 2006
  3. pmc FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments
    Harpreet Kaur Saini
    Computer Science and Engineering Department, 201 Bell Hall University at Buffalo, Buffalo, NY 14260, USA
    Nucleic Acids Res 35:W499-502. 2007
  4. ncbi request reprint Meta-DP: domain prediction meta-server
    Harpreet Kaur Saini
    Center of Excellence in Bioinformatics and Department of Computer Science and Engineering, University at Buffalo, 901 Washington Street, Suite 300, Buffalo, NY 14203, USA
    Bioinformatics 21:2917-20. 2005
  5. pmc Identification and investigation of ORFans in the viral world
    Yanbin Yin
    Computer Science and Engineering Dept, 201 Bell Hall, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Genomics 9:24. 2008
  6. pmc Structural and functional insights into Mimivirus ORFans
    Harpreet Kaur Saini
    Computer Science and Engineering Dept, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Genomics 8:115. 2007
  7. ncbi request reprint The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries
    Daniel Fischer
    Buffalo Center of Excellence in Bioinformatics, University of Buffalo, 901 Washington Street Ste 300, Buffalo, NY 14203, USA
    Bioinformatics 20:2482-4. 2004
  8. ncbi request reprint Structural biology sheds light on the puzzle of genomic ORFans
    Naomi Siew
    Department of Chemistry, Ben Gurion University Beer Sheva 84105, Israel
    J Mol Biol 342:369-73. 2004
  9. pmc LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction
    Leszek Rychlewski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    Protein Sci 14:240-5. 2005
  10. ncbi request reprint A putative novel alpha/beta hydrolase ORFan family in Bacillus
    Naomi Siew
    Department of Chemistry, Ben Gurion University, Beer Sheva 84105, Israel
    FEBS Lett 579:3175-82. 2005

Research Grants

  1. Automated Distant Homology Modeling Meta-server
    Daniel Fischer; Fiscal Year: 2007
  2. Automated Distant Homology Modeling Meta-server
    Daniel Fischer; Fiscal Year: 2009

Detail Information

Publications22

  1. pmc On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
    Yanbin Yin
    Computer Science and Engineering Dept 201 Bell Hall, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Evol Biol 6:63. 2006
    ..Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis...
  2. ncbi request reprint Servers for protein structure prediction
    Daniel Fischer
    Buffalo Center of Excellence in Bioinformatics, and Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY 14260, USA
    Curr Opin Struct Biol 16:178-82. 2006
    ..Recent experiments suggest that servers will soon free humans from most of the burden of protein structure prediction...
  3. pmc FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments
    Harpreet Kaur Saini
    Computer Science and Engineering Department, 201 Bell Hall University at Buffalo, Buffalo, NY 14260, USA
    Nucleic Acids Res 35:W499-502. 2007
    ..Fralanyzer is available at http://fralanyzer.cse.buffalo.edu/...
  4. ncbi request reprint Meta-DP: domain prediction meta-server
    Harpreet Kaur Saini
    Center of Excellence in Bioinformatics and Department of Computer Science and Engineering, University at Buffalo, 901 Washington Street, Suite 300, Buffalo, NY 14203, USA
    Bioinformatics 21:2917-20. 2005
    ..bioinformatics.buffalo.edu/dp/update.html CONTACT: hkaur@bioinformatics.buffalo.edu SUPPLEMENTARY INFORMATION: Available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html...
  5. pmc Identification and investigation of ORFans in the viral world
    Yanbin Yin
    Computer Science and Engineering Dept, 201 Bell Hall, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Genomics 9:24. 2008
    ..Recently, studies attempting to understand the origin and functions of bacterial ORFans have been reported. Here we present a first genome-wide identification and analysis of ORFans in the viral world, with focus on bacteriophages...
  6. pmc Structural and functional insights into Mimivirus ORFans
    Harpreet Kaur Saini
    Computer Science and Engineering Dept, University at Buffalo, Buffalo, NY 14260 2000, USA
    BMC Genomics 8:115. 2007
    ....
  7. ncbi request reprint The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries
    Daniel Fischer
    Buffalo Center of Excellence in Bioinformatics, University of Buffalo, 901 Washington Street Ste 300, Buffalo, NY 14203, USA
    Bioinformatics 20:2482-4. 2004
    ..pl meta-server, which uses top-of-the-line fold-recognition methods. The PDB-Preview provides biologists with preliminary fold assignments well before the experimentally determined 3D structures are released...
  8. ncbi request reprint Structural biology sheds light on the puzzle of genomic ORFans
    Naomi Siew
    Department of Chemistry, Ben Gurion University Beer Sheva 84105, Israel
    J Mol Biol 342:369-73. 2004
    ..Although this survey sheds some light on the ORFan mystery, further experimental studies are required to gain a better understanding of the role and origins of the tens of thousands of ORFans awaiting characterization...
  9. pmc LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction
    Leszek Rychlewski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    Protein Sci 14:240-5. 2005
    ..More importantly, LiveBench-8 identifies a handful of recently developed autonomous (nonmeta) servers that perform at the very top, suggesting that further progress in the individual methods has recently been obtained...
  10. ncbi request reprint A putative novel alpha/beta hydrolase ORFan family in Bacillus
    Naomi Siew
    Department of Chemistry, Ben Gurion University, Beer Sheva 84105, Israel
    FEBS Lett 579:3175-82. 2005
    ..We suggest possible catalytic triads for the ORFans and propose a hypothesis regarding the possible families within the alpha/beta hydrolase superfamily to which they may belong...
  11. pmc The ORFanage: an ORFan database
    Naomi Siew
    Department of Chemistry, Ben Gurion University, Beer Sheva 84105, Israel
    Nucleic Acids Res 32:D281-3. 2004
    ..The ORFanage could help in choosing interesting targets for further genomic and evolutionary studies. The ORFanage is accessible via http://www.bioinformatics.buffalo. edu/ORFanage...
  12. ncbi request reprint LiveBench-6: large-scale automated evaluation of protein structure prediction servers
    Leszek Rychlewski
    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland
    Proteins 53:542-7. 2003
    ..In addition to the growing number of participants, the current experiment marks the introduction of new evaluation procedures, which are aimed to correlate better with functional characteristics of models...
  13. ncbi request reprint Fold-recognition detects an error in the Protein Data Bank
    Janusz Bujnicki
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ks Trojdena, 4 02 109, Warsaw, Poland
    Bioinformatics 18:1391-5. 2002
  14. ncbi request reprint 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 51:434-41. 2003
    ..These improvements represent a step forward toward the wider applicability of fully automated structure-prediction methods at genome scales...
  15. ncbi request reprint 3D-Jury: a simple approach to improve protein structure predictions
    Krzysztof Ginalski
    BioInfoBank Institute, Limanowskiego 24A, 60 744 Poznan, Poland
    Bioinformatics 19:1015-8. 2003
    ..PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)..
  16. ncbi request reprint Modeling three-dimensional protein structures for CASP5 using the 3D-SHOTGUN meta-predictors
    Iris Sasson
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:389-94. 2003
    ..Thus, we conclude that our three goals were achieved. A preliminary automated version of the refinement procedure, named SHGUM, is now available...
  17. ncbi request reprint CAFASP3: the third critical assessment of fully automated structure prediction methods
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:503-16. 2003
    ..This result shows that significant progress has been achieved in automatic structure prediction and has important implications to the prospects of automated structure modeling in the context of structural genomics...
  18. ncbi request reprint 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:517-23. 2003
    ....
  19. ncbi request reprint Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools
    Janusz M Bujnicki
    FEBS Lett 525:174-5. 2002
  20. ncbi request reprint Analysis of singleton ORFans in fully sequenced microbial genomes
    Naomi Siew
    Department of Chemistry, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:241-51. 2003
    ..Further computational and experimental studies aimed at understanding Nature's protein diversity should also include ORFans...
  21. ncbi request reprint The 2002 Olympic Games of protein structure prediction
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva 84015, Israel
    Protein Eng 16:157-60. 2003
    ..We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics...
  22. ncbi request reprint Twenty thousand ORFan microbial protein families for the biologist?
    Naomi Siew
    Department of Chemistry, Department of Computer Science, Ben Gurion University, Beer Sheva 84105, Israel
    Structure 11:7-9. 2003
    ..In this minireview, we draw attention to the increasing number of ORFans and to the consequences of this growth to biological research in the postgenomic era...

Research Grants4

  1. Automated Distant Homology Modeling Meta-server
    Daniel Fischer; Fiscal Year: 2007
    ....
  2. Automated Distant Homology Modeling Meta-server
    Daniel Fischer; Fiscal Year: 2009
    ..abstract_text> ..