Julian Mintseris

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Design of a combinatorial DNA microarray for protein-DNA interaction studies
    Julian Mintseris
    Boston University, Bioinformatics Program, Boston, MA, USA
    BMC Bioinformatics 7:429. 2006
  2. ncbi request reprint Optimizing protein representations with information theory
    Julian Mintseris
    Bioinformatics Program, Boston University, Boston MA 02215, USA
    Genome Inform 15:160-9. 2004
  3. ncbi request reprint Protein-Protein Docking Benchmark 2.0: an update
    Julian Mintseris
    Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA
    Proteins 60:214-6. 2005
  4. ncbi request reprint The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:719-25. 2007
  5. ncbi request reprint ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:207-13. 2005
  6. ncbi request reprint Protein-protein docking: overview and performance analysis
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, MA, USA
    Methods Mol Biol 413:283-314. 2008
  7. ncbi request reprint Integrating statistical pair potentials into protein complex prediction
    Julian Mintseris
    Bioinformatics Program, Boston University, Massachusetts 02215, USA
    Proteins 69:511-20. 2007
  8. pmc Protein-protein docking benchmark version 3.0
    Howook Hwang
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 73:705-9. 2008
  9. ncbi request reprint A protein-protein docking benchmark
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 52:88-91. 2003
  10. pmc Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions
    K G Guruharsha
    Department of Cell Biology Harvard Medical School, Boston, MA, USA
    Fly (Austin) 6:246-53. 2012

Collaborators

Detail Information

Publications18

  1. pmc Design of a combinatorial DNA microarray for protein-DNA interaction studies
    Julian Mintseris
    Boston University, Bioinformatics Program, Boston, MA, USA
    BMC Bioinformatics 7:429. 2006
    ..Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification...
  2. ncbi request reprint Optimizing protein representations with information theory
    Julian Mintseris
    Bioinformatics Program, Boston University, Boston MA 02215, USA
    Genome Inform 15:160-9. 2004
    ..Implications for further structural studies are discussed...
  3. ncbi request reprint Protein-Protein Docking Benchmark 2.0: an update
    Julian Mintseris
    Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA
    Proteins 60:214-6. 2005
    ..The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2...
  4. ncbi request reprint The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:719-25. 2007
    ..Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted...
  5. ncbi request reprint ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:207-13. 2005
    ..These results are evidence that ZDOCK in combination with RDOCK is capable of making accurate predictions on a diverse set of protein complexes...
  6. ncbi request reprint Protein-protein docking: overview and performance analysis
    Kevin Wiehe
    Bioinformatics Program, Boston University, Boston, MA, USA
    Methods Mol Biol 413:283-314. 2008
    ..Finally, we perform regression analysis to better understand the strengths and weaknesses of ZDOCK and to suggest areas of future development for protein-docking algorithms in general...
  7. ncbi request reprint Integrating statistical pair potentials into protein complex prediction
    Julian Mintseris
    Bioinformatics Program, Boston University, Massachusetts 02215, USA
    Proteins 69:511-20. 2007
    ..Furthermore, we show that the new potential performs well on antibody-antigen complexes, with most predictions clustering around the Complementarity Determining Regions of antibodies without any manual intervention...
  8. pmc Protein-protein docking benchmark version 3.0
    Howook Hwang
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 73:705-9. 2008
    ..0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark...
  9. ncbi request reprint A protein-protein docking benchmark
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 52:88-91. 2003
    ..The benchmark is available at (http://zlab.bu.edu/~rong/dock/benchmark.shtml)...
  10. pmc Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions
    K G Guruharsha
    Department of Cell Biology Harvard Medical School, Boston, MA, USA
    Fly (Austin) 6:246-53. 2012
    ..We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map...
  11. ncbi request reprint ZDOCK predictions for the CAPRI challenge
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 52:68-73. 2003
    ..Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed...
  12. pmc A protein complex network of Drosophila melanogaster
    K G Guruharsha
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 147:690-703. 2011
    ..The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution...
  13. pmc Structure, function, and evolution of transient and obligate protein-protein interactions
    Julian Mintseris
    Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 102:10930-5. 2005
    ..In contrast, the plasticity inherent in transient interactions leads to an increased rate of substitution for the interface residues and leaves little or no evidence of correlated mutations across the interface...
  14. ncbi request reprint Atomic contact vectors in protein-protein recognition
    Julian Mintseris
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:629-39. 2003
    ..With this method, we arrive at a nonredundant set of 209 recognition complexes--the largest set reported so far...
  15. pmc Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome
    Craig R Braun
    Department of Pediatric Oncology, Dana Farber Cancer Institute and Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Chem Biol 17:1325-33. 2010
    ..The crosslinking ╬▒ helices covalently trap both static and dynamic protein interactors, and enable rapid identification of interaction sites, providing a critical link between interactome discovery and targeted drug design...
  16. pmc Phosphoproteome analysis of Drosophila melanogaster embryos
    Bo Zhai
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Proteome Res 7:1675-82. 2008
    ..63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events...
  17. pmc Predictome: a database of putative functional links between proteins
    Joseph C Mellor
    Bioinformatics Graduate Program and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 30:306-9. 2002
    ..As a repository for such data, Predictome is an ongoing resource for the community, providing functional relationships among proteins as new genomic data emerges. Predictome is available at http://predictome.bu.edu...
  18. pmc Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    Daniel R Caffrey
    Pfizer Discovery Technology Center, Cambridge, Massachusetts 02139, USA
    Protein Sci 13:190-202. 2004
    ....