Review



fft based sampling program piper  (Acpharis Inc)

 
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 90
      Buy from Supplier

    Structured Review

    Acpharis Inc fft based sampling program piper
    Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform <t>(FFT)</t> based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs <t>PIPER</t> energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003
    Fft Based Sampling Program Piper, supplied by Acpharis Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fft+based+sampling+program+piper/fft+based+sampling+program+piper/pmc03978769-422-8-4
    Average 90 stars, based on 1 article reviews
    fft based sampling program piper - by Bioz Stars, 2026-10
    90/100 stars

    Images

    1) Product Images from "Encounter complexes and dimensionality reduction in protein–protein association"

    Article Title: Encounter complexes and dimensionality reduction in protein–protein association

    Journal: eLife

    doi: 10.7554/eLife.01370

    Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs PIPER energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003
    Figure Legend Snippet: Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs PIPER energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003

    Techniques Used: Generated, Sampling

    Related Articles

    other:

    Article Title: What Method to Use for Protein-Protein Docking?
    Article Snippet: Acpharis Inc. offers commercial licenses to PIPER, the docking program in the ClusPro server.

    Article Title: The ClusPro AbEMap web server for the prediction of antibody epitopes
    Article Snippet: COMPETING INTERESTS The PIPER docking program, on which the ClusPro AbEMap server is based, has been licensed by Boston University to Acpharis Inc. Acpharis, in turn, offers commercial sublicenses of PIPER.

    Article Title: The ClusPro AbEMap web server for the prediction of antibody epitopes.
    Article Snippet: The PIPER docking program, on which the ClusPro AbEMap server is based, has been licensed by Boston University to Acpharis Inc. Acpharis, in turn, offers commercial sublicenses of PIPER.

    Article Title: Mapping of antibody epitopes based on docking and homology modeling.
    Article Snippet: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA Innopolis University, Innopolis, Russia Department of Genome Informatics, Osaka University, Osaka, Japan Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan Department of Mathematics, CUNY Queens College, Flushing, New York, USA

    Sampling:

    Article Title: Encounter complexes and dimensionality reduction in protein–protein association
    Article Snippet: DK: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use. .. DRH: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use. .. DB: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use.

    Article Title: Encounter complexes and dimensionality reduction in protein–protein association
    Article Snippet: DB: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use. .. SV: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use. ..

    Article Title: Encounter complexes and dimensionality reduction in protein–protein association
    Article Snippet: .. DK: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use. .. DRH: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use.



    Similar Products

    fft based sampling program piper  (Acpharis Inc)
    90
    Acpharis Inc fft based sampling program piper
    Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform <t>(FFT)</t> based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs <t>PIPER</t> energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003
    Fft Based Sampling Program Piper, supplied by Acpharis Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fft+based+sampling+program+piper/fft+based+sampling+program+piper/pmc03978769-420-8-4
    Average 90 stars, based on 1 article reviews
    fft based sampling program piper - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs PIPER energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003

    Journal: eLife

    Article Title: Encounter complexes and dimensionality reduction in protein–protein association

    doi: 10.7554/eLife.01370

    Figure Lengend Snippet: Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. ( A ) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn + and E32C-EDTA-Mn 2+ on HPr are encircled and are shown in red and blue, respectively. ( B ) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows ( 8 ): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. ( C ) Ligand IRMSD vs PIPER energy score. ( D ) Two representative HPr poses, colored light blue and dark blue, from Class I. ( E ) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. ( F ) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). ( G ) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view. DOI: http://dx.doi.org/10.7554/eLife.01370.003

    Article Snippet: DK: Owns stock in Acpharis Inc which licensed FFT based sampling program PIPER for commerical use.

    Techniques: Generated, Sampling