Daniel Fischer
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PUBLICATIONS

• PubMed entries
• Publications sorted by research topics and by most cited

Publications by Year:

• 2007 2006
• 2005 2004
• 2003 2002
• 2001 2000
• 1999 1998
• 1997 1996
• 1995 1994
• 1993 1992

2007

• 59. Saini, H.K. and Fischer, D. Structural and functional insights into Mimivirus ORFans. BMC Genomics; 8:115, 2007.

2006

• 58. Yin, Y and Fischer, D. On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. BMC Evolutionary Biol.; 6:63, 2006.


• 57. Fischer, D. Servers for Protein Structure Prediction. Curr. Opin. Struc. Biol; 16:178-182, 2006.



2005

• 56. Siew, N., Saini, H.K. and Fischer, D. A Putative Novel Alpha/Beta Hydrolase Family in Bacillus. FEBS Letters; 579:3175-82, 2005.
• 55. Saini, H.K. and Fischer, D. Meta-DP: Domain Prediction Meta Server. Bioinformatics; 21:2917-2920, 2005.
• 54. Rychlewski, L. and Fischer, D. LiveBench-8: The large-scale, continuous assessment of Automated Protein Structure Prediction. Protein Science; 14:240-245, 2005.

2004

• 53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the Puzzle of Genomic ORFans. J. Mol. Biol; 342:369-373, 2004.
• 52. Fischer, D., Pas, J. and Rychlewski, L. The PDB-Preview Database: A Repository of In-Silico Models of “on-hold” PDB entries. Bioinformatics; 20:2482-2484, 2004.
• 51. Bujnicki, J.M. and Fischer, D. Meta’ Approaches to Protein Structure Prediction. Chapter in Nucleic Acids and Molecular Biology ; 15:23-34 Janusz M. Bujnicki (Ed.). Practical Bioinformatics. Springer-Verlag Berlin Heidelberg, 2004.
• 50. Shmuely, H., Dinitz, E., Dahan, I., Eichler, J., Fischer, D. and Shaanan, B. Poorly-conserved ORFs in the genome of the archaeon Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics; 20:1-6, 2004.
• 49. Siew, N., Azaria, Y. and Fischer, D. The ORFanage: an ORFan database. Nucleic Acids Research; 32:D281-D283, 2004.

2003

• 48. Fischer D, Rychlewski L, Dunbrack RL, Ortiz, AR, Elofsson A. CAFASP3: The Third Critical Assessment of Fully Automated Structure Prediction Methods. Proteins; 53:503-516, 2003
• 47. Fischer D. 3DS3 and 3DS5 3D-SHOTGUN Meta-Predictors in CAFASP3 PROTEINS: Structure, Function, and Genetics; 53:517-523, 2003.
• 46. Rychlewski L, Fischer D, Elofsson A. LiveBench-6: Large-Scale Automated Evaluation of Protein Structure Prediction Servers. PROTEINS: Structure, Function, and Genetics; 53:542-547, 2003.
• 45. Siew N, Fischer D. Unravelling the ORFan puzzle. Comparative and Functional Genomics; 4:432-441, 2003.
• 44. Rychlewski, L, Bujnicki, J, Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. Chapter in The New Avenues in Bioinformatics, Editors: Joseph Seckbach and Eitan Rubin, 2003.
• 43. Sasson I, Fischer D. Modeling Three-Dimensional Protein Structures for CASP5 using the 3D-SHOTGUN Meta-Predictors. PROTEINS: Structure, Function, and Genetics; 53:389-394, 2003.
• 42. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics; 19:1015-1018, 2003.
• 41. Siew N, Fischer D. Analysis of Singleton ORFans in Fully Sequenced Microbial Genomes. PROTEINS: Structure, Function, and Genetics; 53:241-251, 2003.
• 40. Fischer D, Rychlewski, L. The 2002 Olympic Games of Protein Structure Prediction. Protein Engineering; 16:157-160, 2003.
• 39. Siew N, Fischer D. Twenty Thousand ORFan microbial protein families for the biologist? Structure; 11:7-9, 2003.
• 38. Fischer D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. PROTEINS: Structure, Function, and Genetics; 51:434-441, 2003.

2002

• 37. Bujnicki J, Feder M, Rychlewski L, Fischer D. Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools. FEBS Letters; 525:174-175, 2002.
• 36. Bujnicki J, Rychlewski L, Fischer D. Fold-recognition detects an error in the Protein Data Bank. Bioinformatics; 18:1391-1395, 2002.
• 35. Siew N, Fischer D. A user's guide to fold recognition. Chapter in Protein Structure Prediction, IUL Biotechnology Series, Editor Igor F. Tsigelny, International University Line, La Jolla, California. Pages 355-376, 2002.

2001

• 34. Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. BMC Bioinformatics; 2:5, 2001.
• 33. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. Structure prediction meta server. Bioinformatics; 17: 750-751, 2001.
• 32. Fischer D, et al. CAFASP2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. PROTEINS: Structure, Function, and Genetics Suppl.; 5:171-183, 2001.
• 31. Bujnicki JM and Elofsson A, Fischer D and Rychlewski L. LiveBench-2: Large-Scale Automated Evaluation of Protein Structure Prediction Servers. PROTEINS: Structure, Function, and Genetics Suppl.; 5:184-191, 2001.
• 30. Siew N and Fischer D. Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP. IBM Systems Journal; 40:No.2, 410-425, 2001.
• 29. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. LiveBench-1: Continuous benchmarking of protein structure prediction servers. Protein Science; 10:352-361, 2001.
• 28. Fischer D, Baker D, Moult J. We need both computer models and experiments. Nature; 409:558, 2001.

2000

• 27. Fischer D, Elofsson A, Rychlewski L. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2. Protein Engineering; 13:667-670, 2000.
• 26. Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics; 16:776-785, 2000.
• 25. Fischer D. Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information. Pacific Symp Biocomputing, Hawaii; 119-130, January 2000.

1999

• 24. Fischer D. Rational structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Protein Engineering; 12:1029-1030, 1999.
• 23. Fischer D, Eisenberg D. Predicting structures for genome proteins. Current Opinion in Structural Biology; 9:208-211, 1999.
• 22. Fischer D. Modeling Three-Dimensional Protein Structures for amino acid sequences of the CASP3 experiment using Sequenced-Derived Predictions. PROTEINS: Structure, Function, and Genetics Suppl.; 3:61-65, 1999.
• 21. Fischer D, et al. CAFASP-1: Critical Assessment of Fully Automated Structure Prediction Methods. PROTEINS: Structure, Function, and Genetics Suppl.; 3:61-65, 1999.
• 20. Fischer D, Eisenberg D. Finding families for genomic ORFans. Bioinformatics; 15:759-762, 1999.
• 19. Landgraf R, Fischer D, Eisenberg D. Analysis of heregulim symmetry by weighted evolutionary tracing. Protein Engineering; 12:943-951, 1999.

1998

• 18. Beamer L, Fischer D, Eisenberg D. Detecting distant relatives of mammalian LPS-binding and lipid transport proteins. Protein Science; 7:1643-1646, 1998.

1997

• 17. Fischer D, Eisenberg D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc. Natl. Acad. Sci.; 94:11929-11934, 1997.
• 16. Rice DW, Fischer D, Weiss R, Eisenberg D. Fold Assignments for Amino Acid Sequences of the CASP2 Experiment. PROTEINS: Structure, Function, and Genetics, Suppl.; 1:113-122, 1997.

1996

• 15. Elofsson A, Fischer D, Rice DW, LeGrand S, Eisenberg D. A study of combined structure/sequence profiles. Folding & Design; 1:451-461, 1996.
• 14. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Science; 5:947-955, 1996.
• 13. Fischer D, Rice DW, Bowie JU, Eisenberg D. Assigning amino acid sequences to 3-dimensional protein folds. FASEB Journal; 10:126-136, 1996.
• 12. Fischer D , Elofsson A, Rice DW, Eisenberg D. Assessing the Performance of Fold Recognition Methods By Means of a Comprehensive Benchmark. Pacific Symp Biocomputing, Hawaii; 300-318, January 1996.
• 11. Alexandrov NN, Fischer D. Analysis of Topological and Nontopological Structural Similarities in the PDB: New Examples With Old Structures. PROTEINS: Structure, Function and Genetics; 25:354-365, 1996.
• 10. Naor D, Fischer D, Jernigan RL, Wolfson HJ, Nussinov R. Amino Acid Pair Interchanges at Spatially Conserved Locations. J. Mol. Biol.; 256:924-938, 1996.

1995

• 9. Fischer D, Tsai CJ, Nussinov R, Wolfson H. A 3D sequence-independent representation of the protein data bank. Protein Engineering; 8:981-997, 1995.
• 8. Fischer D, Lin SL, Wolfson H, Nussinov R. A Geometry-based Suite of Molecular Docking Processes. J. Mol. Biol.; 248:459-477, 1995.

1994

• 7. Norel R, Fischer D, Wolfson H, Nussinov R. Molecular surface recognition by a computer vision-based technique. Protein Engineering; 7:39-46, 1994.
• 6. Lin LS, Nussinov R, Fischer D, Wolfson H. Molecular Surface Representations by Sparse Critical Points. PROTEINS: Structure, Function and Genetics; 18:94-101, 1994.
• 5. Fischer D, Wolfson H, Lin SL, Nussinov R. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding. Protein Science; 3:769-768, 1994.

1993

• 4. Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Engineering; 6:279-288, 1993.
• 3. Fischer D, Norel R, Wolfson H, Nussinov R. Surface Motifs by a Computer Vision Technique: Searches, Detection, and Implications for Protein-Ligand Recognition. PROTEINS: Structure, Function, and Genetics; 16:278-292, 1993.
• 2. Fischer D, Wolfson H, Nussinov R. Spatial, Sequence-Order-Independent Structural Comparison of a/b Proteins: Evolutionary Implications. Journal of Biomolecular Structure & Dynamics; 11:367-380, 1993.

1992

• 1. Fischer D, Bachar O, Nussinov, R, Wolfson, H. An Efficient Automated Computer Vision Based Technique for Detection of Three Dimensional Structural Motifs in Proteins. Journal of Biomolecular Structure & Dynamics; 9:769-789, 1992.