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Citations relating to MACiE

MACiE was first released in 2005, with Version 2 being release in 2007 and Version 3 released in 2011:

    2011

  1. M. Shokhen et al. The mechanism of papain inhibition by peptidyl aldehydes. Proteins: Structure, Function and Bioformatics, 79, 975-985. 2011 PubMed ID: 21181719
  2. K. Prymula et al. Catalytic residues in hydrolases: Analysis of methods designed for ligand-binding site prediction. Journal of Computer-Aided Molecular Design, 25, 117-133. 2011 PubMed ID: 21104192
  3. J. B. O. Mitchell. Informatics, machine learning and computational medicinal chemistry. Future Medicinal Chemistry, 3, 451-467. 2011 PubMed ID: 21452981
  4. D. E. Almonacid and P. C. Babbitt. Toward mechanistic classification of enzyme functions. Current Opinion in Chemical Biology, 15, 435-442. 2011 PubMed ID: 21489855
  5. 2010

  6. J. C. Triviño and F. Pazos. Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. BMC Systems Biology, 4 Art. No. 46. 2010 PubMed ID: 20406431
  7. H. R. Ansari and G. P. S. Raghava. Identification of NAD interacting residues in proteins. BMC Bioinformatics, 11, Art. No. 160. 2010 PubMed ID: 20353553
  8. D. E. Almonacid et al. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: Implications for classification of enzyme function. PLoS Computational Biology, 6(3). 2010 PubMed ID:20300652
  9. J. D. Pollack et al. Concentration of Specific Amino Acids at the Catalytic/Active Centers of Highly-Conserved "Housekeeping" Enzymes of Central Metabolism in Archaea, Bacteria and Eukaryota: Is There a Widely Conserved Chemical Signal of Prebiotic Assembly? Origins of Life and Evolution of Biospheres, 40, 273-302. 2010 PubMed ID:20069373
  10. M. V. Omelchenko et al. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution. Biology Direct, 5; Art. No. 31. 2010 PubMed ID: 20433725
  11. X. Y. Hu et al. Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods. Journal of Chemical Information and Modeling, 50, 1089-1100. 2010 PubMed ID: 20515020
  12. N. J. Harmer. The Structure of Sedoheptulose-7-Phosphate Isomerase from Burkholderia pseudomallei Reveals a Zinc Binding Site at the Heart of the Active Site. Journal of Molecular Biology, 400, 379-392. 2010 PubMed ID: 20447408
  13. J. D. Fischer et al. The CoFactor database: Organic cofactors in enzyme catalysis. Bioinformatics, 26, 2496-2497. 2010 PubMed ID: 20679331
  14. J. D. Fischer et al. The Structures and Physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology, 403, 803-824. 2010 PubMed ID: 20850456
  15. 2009

  16. G. A. Reeves et al. Genome and proteome annotation: Organization, interpretation and integration. Journal of the Royal Society Interface, 6, 129-147. 2009 PubMed ID: 19019817
  17. G. L. Holliday et al. Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology, 390, 560-577. 2009 PubMed ID: 19447117
  18. J. Smith and V. Stein. SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design. Computational Biology and Chemistry, 33 149-159. 2009 PubMed ID: 19157988
  19. T. Bray et al. Sequence and Structural Features of Enzymes and their Active Sites by EC Class. Journal of Molecular Biology, 386, 1423-1436. 2009 PubMed ID: 19100748
  20. D. Talavera et al. WSsas: a web service for the annotation of functional residues through structural homologues. Bioinformatics, 25, 1192-1194. 2009 PubMed ID: 19251774
  21. A. J. T. Smith et al. Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2. Organic & Biomolecular Chemistry, 7, 2716-2724. 2009 PubMed ID: 19532987
  22. B. H. Dessailly and C. A. Orengo. Function Diversity Within Folds and Superfamilies (Book chapter) 2009; From Protein Structure to Function with Bioinformatics; Springer Netherlands; 143-166. DOI 10.1007/978-1-4020-9058-5
  23. O. Sacher et al. Investigations of Enzyme-Catalyzed Reactions Based on Physicochemical Descriptors Applied to Hydrolases. Journal of Chemical Information and Modeling, 49, 1525-1534. 2009 PubMed ID: 19445497
  24. S. Yeniterzi and U. Sezerman. EnzyMiner: Automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. BMC Bioinformatics, 10 (SUPPL. 8), art. no. S2. 2009 PubMed ID: 19758466
  25. A. Y. Mulkidjanian and M. Y. Galperin. On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biology Direct, 4, Art. No. 27. 2009 PubMed ID: 19703275
  26. D. T. Manallack. The acid-base profile of a contemporary set of drugs: Implications for drug discovery. SAR and QSAR in Environmental Research, 20, 611-655. 2009 PubMed ID: 20024802
  27. C. Andreini et al. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics, 25, 2088-2089. 2009PubMed ID: 19369503
  28. Z. D. Zhang et al. An Overview of the De Novo Prediction of Enzyme Catalytic Residues. Current Bioinformatics, 4, 197-206. 2009
  29. 2008

  30. X. Zhang et al. Quantum mechanical design of enzyme active sites. Journal of Organic Chemistry, 73, 889-899. 2008 PubMed ID: 18179229
  31. C. Andreini et al. Metal ions in biological catalysis: From enzyme databases to general principles. Journal of Biological Inorganic Chemistry, 13, 1205-1218. 2008 PubMed ID: 18604568
  32. O. C. Redfern et al. Exploring the structure and function paradigm. Current Opinion in Structural Biology, 18, 394-402. 2008 PubMed ID: 18554899
  33. J. Apostolakis et al. Automatic determination of reaction mappings anal reaction center information. 2. Validation on a biochemical reaction database. Journal of Chemical Information and Modeling, 48, 1190-1198. 2008 PubMed ID: 18533714
  34. R. A. Chiang et al.. Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Comput Biol., 4. 2008 PubMed ID: 18670595
  35. M. Punta and Y. Ofran. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol., 4. 2008 PubMed ID: 18974821
  36. R. Alves et al. Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology. Current Bioinformatics, 3, 98-129. 2008
  37. 2007

  38. G. L. Holliday et al. The chemistry of protein catalysis. Journal of Molecular Biology, 372, 1261-1277. 2007 PubMed ID: 17727879
  39. J. W. Torrance et al. The geometry of interactions between catalytic residues and their substrates. Journal of Molecular Biology, 369, 1140-1152. 2007 PubMed ID: 17466330
  40. I. T. Horváth and P. T. Anastas. Innovations and green chemistry. Chemical Reviews, 107, 2169-2173. 2007 PubMed ID: 17564478
  41. S. Gupta and J. Aires-de-Sousa. Comparing the chemical spaces of metabolites and available chemicals: Models of metabolite-likeness. Molecular Diversity, 11, 23-36. 2007 PubMed ID: 17447158
  42. N. M. O'Boyle et al. Using reaction mechanism to measure enzyme similarity. Journal of Molecular Biology, 368, 1484-1499. 2007 PubMed ID: 17400244
  43. 2006

  44. A. K. Arakaki et al. High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC Genomics, 7. 2006 PubMed ID: 17166279
  45. I. A. Gariev and S. D. Varfolomeev. Hierarchical classification of hydrolases catalytic sites. Bioinformatics, 22, 2574-2576. 2006 PubMed ID: 16877756
  46. M. E. Glasner et al.. Evolution of enzyme superfamilies. Current Opinion in Chemical Biology, 10, 492-497. 2006 PubMed ID: 16935022
  47. E. L. Willighagen et al. Molecular chemometrics. Critical Reviews in Analytical Chemistry, 36, 189-198. 2006 DOI: 10.1080/10408340600969601
  48. S. C-H Pegg et al. Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database. Biochemistry, 45, 2545-2555. 2006 PubMed ID: 16489747

Citations relating to Metal-MACiE

Metal-MACiE was first released in 2009:

    2011

  1. D. E. Almonacid and P. C. Babbitt. Toward mechanistic classification of enzyme functions. Current Opinion in Chemical Biology, 15, 435-442. 2011 PubMed ID: 21489855
  2. 2010

  3. I. Bertini and G. Cavallaro. Bioinformatics in bioinorganic chemistry. Metallomics, 2; 39-51. 2010 PubMed ID: 21072373
  4. K. Nakamura et al. Metalmine: A database of functional metal-binding sites in proteins. Plant Biotechnology, 26, 517-521. 2010.
  5. D. E. Almonacid et al. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: Implications for classification of enzyme function. PLoS Computational Biology, 6(3). 2010 PubMed ID:20300652
  6. M. V. Omelchenko et al. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution. Biology Direct, 5; Art. No. 31. 2010 PubMed ID: 20433725
  7. J. D. Fischer et al. The CoFactor database: Organic cofactors in enzyme catalysis. Bioinformatics, 26, 2496-2497. 2010 PubMed ID: 20679331
  8. A. Cvetkovic et al. Microbial metalloproteomes are largely uncharacterized. Nature, 466, 779-782. 2010 PubMed ID: 20639861

Citations relating to CoFactor

CoFactor was first released in 2010:

    2011

  1. D. E. Almonacid and P. C. Babbitt. Toward mechanistic classification of enzyme functions. Current Opinion in Chemical Biology, 15, 435-442. 2011 PubMed ID: 21489855
  2. 2010

  3. J. D. Fischer et al. The Structures and Physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology, 403, 803-824. 2010 PubMed ID: 20850456


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