Daniel Fischer

Daniel Fischer
Research Group

PUBLICATIONS BY RESEARCH TOPICS

The following is a list of my publications organized by subject areas. Within each topic, the most relevant ones appear first. Some publications are included in more than one subject area. The numbers correspond to the chronological order of publication (higher is more recent).

The subject areas used are:

Most Cited Papers
Meta 3D protein structure prediction
Genomic ORFans and Evolution
Protein Structure Prediction Methods
Bioinformatics and Structure Determination
Genome-wide Structural Assignments, Structural Genomics
Assessment of Structure Prediction Methods: Benchmarks, Assesment Methods
CASP "winner" papers
Structure Comparison
Docking
Reviews

Miscelaneous Topics

Most Cited Papers (as of Mar. 2005 in ISI). Papers with more than 35 citations are ranked in the top 1% within the field according to the Essential Science Indicators. About one third of my papers fall in this category, with over 26 papers each having 26 citations or more (h-number). Notice that higher-impact, recently published papers may not have had time to accumulate enough citations. The 10 most cited papers together have accumulated over 1100 citations, or 110 citations per paper on average. The papers with most citations are listed first.
- Over 100 citations:
  - 14. Fischer, D. and Eisenberg, D. Protein Fold Recognition Using Sequence-Derived Properties. Protein Science, 5: 947-955, 1996.
  - 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.
  - 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.
  - 33. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. Structure prediction meta server. Bioinformatics 17, 750-751, 2001.
- Over 80 citations:
  - 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.
  - 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.
- Over 40 citations:
  - 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.
  - 26. Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. MaxSub: A Measure for Quality Assessment of Protein Structure Predictions. Bioinformatics 16:776-785, 2000.
  - 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.
  - 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.
  - 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.
  - 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.
  - 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.
  - 20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.
  - 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.
  - 11. Alexandrov, N.N. and 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.
  - 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.
  - 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor.
  - 7. Norel, R., Fischer, D., Wolfson, H & Nussinov, R. Molecular Surface Recognition by a Computer Vision Based Technique. Protein Engineering, 7, 39-46, 1994.
  - 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.
Meta 3D protein structure prediction
- 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins, 51:434-441, 2003.
- 47. Fischer, D. The 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins, 53: 517-523, 2003.
- 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.
- 33. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. Structure prediction meta server. Bioinformatics 17, 750-751, 2001.
- 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.
- 55. Saini, H.K. and Fischer, D. Meta-DP: Domain Prediction Meta Server. Bioinformatics; 21:2917-2920, 2005.
- 59. Saini, H.K. and Fischer, D. Structural and functional insights into Mimivirus ORFans. BMC Genomics; 8:115, 2007.
Genomic ORFans and Evolution
- 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.
- 39. Siew, N and Fischer, D. 20,000 ORFan microbial protein families for the biologist? Structure , 11: 7-9, 2003.
- 41. Siew, N and Fischer, D. Analysis of Singleton ORFans in Fully Sequenced Microbial Genomes. Proteins, 53: 241-251, 2003.
- 53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the ORFan Puzzle. J. Mol. Biol., 342:369-373, 2004.
- 20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.
- 45. Siew, N. and Fischer, D. Unravelling the ORFan puzzle. Comparative and Functional Genomics, 4: 432-441, 2003.
- 24. Fischer, D. Structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Prot. Eng., 12:1029-1030, 1999.
- 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.
- 49. Siew, N., Azaria, Y. and Fischer, D. The ORFanage: An ORFan Database. Nucl. Acid. Research, 32,D281-D283, 2004.
- 56. Siew, N., Saini, H.K. and Fischer, D. A Putative Novel Alpha/Beta Hydrolase Family in Bacillus. FEBS Letters; 579:3175-82, 2005.
- 59. Saini, H.K. and Fischer, D. Structural and functional insights into Mimivirus ORFans. BMC Genomics; 8:115, 2007.
Protein Structure Prediction Methods
- 57. Fischer, D. Servers for Protein Structure Prediction. Curr. Opin. Struc. Biol; 16:178-182, 2006.
- 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins, 51:434-441, 2003.
- 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
- 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.
- 14. Fischer, D. and Eisenberg, D. Fold Recognition Using Sequence-Derived Properties. Protein Science, 5, 947-955, 1996.
- 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.
- 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.
- 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.
Bioinformatics and Structure Determination
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.

28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001.

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.

44. Rychlewski, L, Bujnicki, J and Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. Chapter in, Book in press, 2003.
Genome-wide Structural Assignments, Structural Genomics
53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the ORFan Puzzle. J. Mol. Biol., 342:369-373, 2004.

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.

23. Fischer, D. and Eisenberg, D. Predicting structures for genome proteins. Curr. Opin. Structural Biology, 9:208-211, 1999.

28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001.

24. Fischer, D. Structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Prot. Eng., 12:1029-1030, 1999.

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.

20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.

59. Saini, H.K. and Fischer, D. Structural and functional insights into Mimivirus ORFans. BMC Genomics; 8:115, 2007.
Assessment of Structure Prediction Methods: Benchmarks, Assesment Methods
CAFASP / LiveBench series

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

54. Rychlewski, L and Fischer, D. LiveBench-8: The large-scale, continuous assessment of Automated Protein Structure Prediction. Protein Science , in press, 2004.

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.

46. Rychlewski, L. Fischer, D. and Elofsson, A. LiveBench-6: Large-Scale Evaluation of Protein Structure Prediction Servers. Proteins, 53: 542-547, 2003.

40. Fischer,D and Rychlewski, L. The 2002 Olympic Games of Protein Structure Prediction Prot. Eng., 16: 157-160, 2003.

32. Fischer, D., et al. CAFASP-2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, Suppl. 5, 171-183, 2001.

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.

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.

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.

28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001.

27. Fischer, D., Elofsson, A. and Rychlewski, L. The 2000 Olympic Games of Protein Structure Prediction. Prot. Eng. , 13(10):667-670, 2000.

21. Fischer, D et al. Critical Assessment of Fully Automated Structure Prediction Methods - CAFASP1, Proteins, Dedicated CASP3 issue, 1999.

Assessment Methods

26. Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. MaxSub: A Measure for Quality Assessment of Protein Structure Predictions. Bioinformatics 16:776-785, 2000.

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.

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.
CASP "winner" papers
47. Fischer, D. The 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins, 53: 517-523, 2003.

43. Sasson, I and Fischer, D. Modeling Three-Dimensional Protein Structures for CASP5 Using the 3D-SHOTGUN meta-predictors. Proteins, 53: 389-394, 2003.

32. Fischer, D., et al. CAFASP-2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, Suppl. 5, 171-183, 2001.

22. Fischer, D. Modeling 3D Protein Structures for the CASP3 experiment. Proteins, Dedicated CASP3 issue, 1999.

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.
Structure Comparison
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.

11. Alexandrov, N.N. and 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.

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.

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.

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.

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.

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.

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.
Docking
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.

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.

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

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. In press, 2004.

45. Siew, N. and Fischer, D. Unravelling the ORFan puzzle. Comparative and Functional Genomics, 4: 432-441, 2003.

44. Rychlewski, L, Bujnicki, J and Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. Chapter in, Book in press, 2003.

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.

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.

23. Fischer, D. and Eisenberg, D. Predicting structures for genome proteins. Curr. Opin. Structural Biology, 9:208-211, 1999.

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.
Miscelaneous Topics
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.

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.

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.

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