• 2004
  
  
  • 54. Rychlewski, L and Fischer, D. LiveBench-8: The large-scale, continuous assessment of Automated Protein Structure Prediction. Protein Science , in press, 2004.
    
    
  • 53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the ORFan Puzzle. J. Mol. Biol., 342:369-373, 2004. pdf .
    
    
  • 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. and Fischer, D. Meta Approaches to Protein Structure Prediction. Chapter in Nucleic Acids and Molecular Biology, Vol. 15. pp 23-34. Janusz M. Bujnicki (Ed.). Practical Bioinformatics. Springer-Verlag Berlin Heidelberg, 2004. pdf .
    
    
  • 50. Shmuely, H., Dinitz, E., Dahan, I., Eichler, J., Fischer, D. and Shaanan, B. Poorly-conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics, 20: 1248-1253, 2004. pdf .
    
    
  • 49. Siew, N., Azaria, Y. and Fischer, D. The ORFanage: An ORFan Database. Nucl. Acid. Research, 32,D281-D283, 2004. NAR .
    
    
  
  
• 2003
  
  
  • 48. Fischer, D., Rychlewski, L., Dunbrack, R. L., Ortiz, A. R. and Elofsson, A. CAFASP3: The Third Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, 53: 503-516, 2003. pdf .
    
    
  • 47. Fischer, D. The 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins, 53: 517-523, 2003. pdf .
    
    
  • 46. Rychlewski, L. Fischer, D. and Elofsson, A. LiveBench-6: Large-Scale Evaluation of Protein Structure Prediction Servers. Proteins, 53: 542-547, 2003. pdf .
    
    
  • 45. Siew, N. and Fischer, D. Unravelling the ORFan puzzle. Comparative and Functional Genomics, 4: 432-441, 2003. pdf .
    
    
  • 44. Rychlewski, L, Bujnicki, J and Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. In The New Avenues in Bioinformatics, in press, 2004.
    
    
  • 43. Sasson, I and Fischer, D. Modeling Three-Dimensional Protein Structures for CASP5 Using the 3D-SHOTGUN meta-predictors. Proteins, 53: 389-394, 2003. pdf .
    
    
  • 42. Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19: 1015-1018, 2003.
    
    
  • 41. Siew, N and Fischer, D. Analysis of Singleton ORFans in Fully Sequenced Microbial Genomes. Proteins, 53: 241-251, 2003. pdf .
    
    
  • 40. Fischer,D and Rychlewski, L. The 2002 Olympic Games of Protein Structure Prediction Prot. Eng., 16: 157-160, 2003. pdf .
    
    
  • 39. Siew, N and Fischer, D. 20,000 ORFan microbial protein families for the biologist? Structure , 11: 7-9, 2003. pdf .
    
    
  • 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins, 51:434-441, 2003. ps.
    
    
• 2002
  
  
  • 37. Janusz Bujnicki, Marcin Feder, Leszek Rychlewski and Daniel Fischer. 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. Janusz Bujnicki, Leszek Rychlewski and Daniel Fischer. Fold-Recognition Detects an Error in the Protein Data Bank. Bioinformatics , 18: 1391-1395, 2002.
    
    
  • 35. Naomi Siew and Daniel Fischer. A user's guide to fold recognition. 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. CAFASP-2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, Suppl. 5, 171-183, 2001. pdf .
    
    
  • 31. Buhnicki, J. M. and Elofsson, A., Fischer, D. and Rychlewski, L. LiveBench-2: The Second Large-Scale Evaluation of Protein Structure Prediction Servers. Proteins, Suppl. 5, 184-191, 2001. pdf .
    
    
  • 30. Siew, N. and Fischer, D. Convergent Evolution of CAFASP and Computer Chess Tournaments: CASP, Kasparov and CAFASP. IBM Systems Journal , 40, No.2, 410-425, 2001. pdf .
    
    
  • 29. Buhnicki, J. M., Elofsson, A., Fischer, D. and Rychlewski, L. LiveBench1: Continuous Benchmarking of Protein Structure Prediction Servers. Prot. Sci. , 10: 352-361, 2001. pdf .
    
    
  • 28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001. ps .
  
  
  
• 2000
  
  
  • 27. Fischer, D., Elofsson, A. and Rychlewski, L. The 2000 Olympic Games of Protein Structure Prediction. Prot. Eng. , 13(10):667-670, 2000.
    
    
  • 26. Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. MaxSub: A Measure for Quality Assessment of Protein Structure Predictions. Bioinformatics 16(9):776-785, 2000. pdf .
    
    
  • 25. Fischer, D. Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information. Pacific Symp. Biocomputing, Hawaii, 119-130, January 2000. Editors: Altman, R.B., Dunker, A.K., Hunter, Lauderdale, K. and Klein, T.E. Publishers: World Scientific. scanned pdf.
  
  
  
• 1999
  • 24. Fischer, D. Rational structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Prot. Eng., 12:1029-1030, 1999.
    
  • 23. Fischer, D. and Eisenberg, D. Predicting structures for genome proteins. Curr. Opin. Structural Biology, 9:208-211, 1999.
    
  • 22. Fischer, D. Modeling 3D Protein Structures for the CASP3 experiment. Proteins, Dedicated CASP3 issue, 1999.
    
  • 21. Fischer, D et al. Critical Assessment of Fully Automated Structure Prediction Methods - CAFASP1, Proteins, Dedicated CASP3 issue, 1999.
    
  • 20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.
    
  • 19. Landgraf, R., Pegram, M., Fischer, D., Slamon, D.J. and Eisenberg, D. Analysis of heregulin symmetry by evolutionary tracing. Prot. Eng, , 12: 943-951, 1999.
• 1998
  • 18. Beamer, L, Fischer, D. and Eisenberg, D. Detecting distant relatives of mammalian LPS-binding and lipid transport proteins. Protein Science , 7,1643-1646, 1998.
• 1997
  • 17. Fischer, D. and Eisenberg, D. Assigning Folds to the Proteins Encoded by the Genome of Mycoplasma genitalium. Proc. Nat. Academy of Sciences, 94, 11929-11934, 1997 pdf.
  • 16. Rice, D.W., Fischer, D., Weiss, R. & Eisenberg, D.. Fold Assignments for Amino Acid Sequences of the CASP2 Experiment. Proteins, Suppl. 1, 113-122, 1997.
• 1996
  • 15. Elofsson, A., Fischer, D., Rice, D.W., LeGrand, S. and Eisenberg, D. A Study of Combined Structure-sequence Profiles. Folding and Design, 1, 451-461, 1996.
  • 14. Fischer, D. and Eisenberg, D. Fold Recognition Using Sequence-Derived Properties. Protein Science, 5, 947-955, 1996.
  • 13. Fischer, D., Rice, D.W., Bowie, J.U. and Eisenberg, D. Assigning Amino Acid Sequences to 3D Protein Folds. FASEB J., 10, 126-136, 1996.
  • 12. Fischer, D., Elofsson, A., Rice, D.W., LeGrand, S. and Eisenberg, D. Assessing the Performance of Fold Recognition Methods By Means of a Comprehensive Benchmark. in Proc. Pacific Symp. Biocomputing, Hawaii, 300-318 January 1996 scanned pdf.
  • 11. Alexandrov, N.N. and Fischer, D. Ensembles of the Similarly Arranged Secondary Structure Elements in Proteins. Proteins: Structure, Function and Genetics, 25, 354-365, 1996.
  • 10. Naor, D., Fischer, D., Jernigan, R. L., Wolfson, H. J. and Nussinov, R. Amino Acid Pair Interchanges at Spatially Conserved Locations. J. Mol. Biol., 256, 924,938,1996.
• 1995
  • 9. Fischer, D., Tsai, C.J., Nussinov, R. and Wolfson, H. A 3-D Sequence-Independent Representation of the Protein Data Bank. Protein Engineering, 8, 981-997, 1995.
  • 8. Fischer, D., Lin, S.L., Wolfson, H. and 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, L. S., Nussinov, R., Fischer, D. and Wolfson, H. Molecular Surface Representation by Sparse Critical Points. Proteins: Structure, Function and Genetics, 18, 94-101, 1994.
  • 5. Fischer, D., Wolfson, H., Lin, S. L. and 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 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., Nussinov, R. & Wolfson, H. Spatial, Sequence-Order Independent Structural Comparison of alpha/beta Proteins: Evolutionary Implications. J. Biom. Struct. & 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. J. Biom. Struct. & Dynamics, 9, 769-789, 1992.

REFEREED CONFERENCE PROCEEDINGS:

• Fischer, D., Lin, L. S., Nussinov, R. and Wolfson, H. Docking of Protein Molecules. 12th. Int. Conf. Pattern Recognition, Jerusalem, Israel, Oct. 1994.
• Fischer, D., Norel, R., Nussinov, R. and Wolfson, H. 3-D Matching and Docking of Protein Molecules. Proc. 4rd. Symp. Comb. on Pattern Matching, Padova, Italy, May 1993. Lecture Notes in Computer Science 684, 20-34, Springer-Verlag.
• Fischer, D., Nussinov, R. & Wolfson, H. 3-D Substructure Matching in Protein Molecules. Proc. 3rd. Symp. Comb. on Pattern Matching, Tucson, Arizona, April 1992. Lecture Notes in Computer Science 644, 133-147, Springer-Verlag.
• Fischer, D., Levhari, Y. & Singer, G. Abstraction of Schematics to High Level RTL. Europ. Data Automation Conf. 1990.

CONFERENCES (traced up to Nov. 1995):

• Fischer, D. and Eisenberg, D. A systematic comparison of inverted protein folding methods using a comprehensive benchmark. 4th. Conf. Mathematics and Molecular Biology, Santa Fe, New Mexico, November 1995.
• Fischer, D. and Eisenberg, D. Advances in assignment of amino acid sequences to 3D protein folds. 4th. Conf. Mathematics and Molecular Biology, Santa Fe, New Mexico, November 1995.
• Le Grand, S., Fischer, D., Rice, D. W. and Eisenberg, D. Conformational encodings: application to sequence search. 4th. Conf. Mathematics and Molecular Biology, Santa Fe, New Mexico, November 1995.
• Eisenberg, D. Bowie, J.U., Luthy, R., Wesson, L., Zhang, K., Wilmanns, M., Rice, D. and Fischer, D. Applications of 3D profiles: assigning amino acid sequences to folds; assessing protein models and refining protein structures. 9th Symp of the Protein Society. Boston, MA, July, 1995.
• Nussinov, R., Fischer, D., Lin, S.L., Naor, D., Tsai, C.J. and Wolfson, H. Searching for structural similarities between protein cores, surfaces and between protein-protein interfaces. 9th Conv. Biomol. Stereodynamics. J. Biom. Struct. & Dynamics, Vol. 12 no. 6, Book of Abstracts, pp. a177, June 1995, Albany NY.
• Nussinov, R., Fischer, D., Lin, S.L., Naor, D., Tsai, C.J., Alexandrov, N. and Wolfson, H. Searching for structural similarities between protein cores, surfaces and between protein-protein interfaces. 9th Symp of the Protein Society. Boston, MA, July, 1995.
• Lin, S.L., Fischer, D., Wolfson, H. and Nussinov, R. Surface description and biomolecular recognition (docking). Book of Abstracts Biophysical Society, Biophysical J. pg. A62, March, 1994.
• Fischer, D., Tsai, C.J., Lin, S.L., Wolfson, H. and Nussinov, R. 3-D, sequence-order-independent comparisons of protein structures. Book of Abstracts Biophysical Society, Biophysical J. pg. A62, March, 1994.
• Lin, S.L., Fischer, D., Tsai, C.J., Wolfson, H. and Nussinov, R. Surface description, biomolecular recognition (docking) and sequence-order independent, substructural motifs in proteins. Book of Abstracts Chemical Society, March, 1994.
• Nussinov, R., Fischer, D., Norel, R. and D., Wolfson, H. 3-D matching and docking of protein molecules. Book of Abstracts Biophysical Society, Biophysical J., Vol. 64, p. A284, February, 1993.
• Nussinov, R., Norel, R., Fischer, D. and Wolfson. Molecular surface recognition by a computer vision based technique. UCLA Keystone Symposia: Prospects and progress in Drug Design Based on peptides and proteins, Taos, New Mexico, J. Cellular Biochemistry, supp. 18c, p. 225, March, 1993.
• Nussinov,R., Lin, S. H., Norel, R., Fischer, D. and Wolfson, H. J. Molecular Surface Recognition by a Computer Vision Based Technique. 8th Conv. Biomol. Stereodynamics. J. Biom. Struct. & Dynamics, vol. 10, Book of Abstracts, pp. a144, Albany NY, June 1993.
• Fischer, D., Nussinov, R. & Wolfson, H. Three-Dimensional Protein Substructural Comparison. Workshop on High performance computing and Grand Challenges in Structural Biology, p. 39, January 1992, Tallahassee, Florida.
• Nussinov, R., Fischer, D., Wolfson, H. A computer vision based 3-D approach for the comparison of protein structures. Book of Abstracts Biophysical Society, Biophysical J., Vol. 61, p. A349, February, 1992.
• Fischer, D., Nussinov, R. & Wolfson, H. 3-D Pattern Matching in Proteins. 6th Symp of the Protein Society. San Diego, Cal, July, 1992.
• Norel, R., Fischer, D., Nussinov, R., Wolfson, H and Maizel, J. 3-D Proteins surface and core substructural matching using a Computer Vision Based Technique. NIH research festival, Sept 21, 1992.
• Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H. An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. 7th Conv. Biomol. Stereodynamics. J. Biom. Struct. & Dynamics, Vol. 6 no. 6, Book of Abstracts, pp. a10, June 1991, Albany NY.

REPORTS:

• Fischer, D. Structural Matching Algorithms in Molecular Biology. Ph.D. Thesis. The Moise and Frida Eshkenasy Inst. of Computer Sciences, 1994.
• Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H. Three-Dimensional Structural Comparison of Proteins by a Computer Vision Based Technique. The Moise and Frida Eshkenasy Inst. of Computer Sciences, Tech. Report 237/92, January 1992.
• Fischer, D. Maintainance of Unreliable Distributed Systems. M.Sc. Thesis Computer Science, Technion, Israel, 1988.