Ask
Search
My library
ORKG

ORKG Ask

Our mission is to organize scholarly knowledge and make it accessible to humans and machines.

About

About ORKG Ask
Report issue
Statistics
Contact

Legal

Terms of use
Data protection (sheet)
Imprint
Accessibility
License

Technical

We
open source
System status
Changelog
Frontend: v1.41.0
Backend: v1.13.4

We use cookies to provide a better user experience.

Data Protection

HLA-A2 super-type binding possibility of selected peptides predicted by NetMHCPan1.1.

Negar Seyed (344790)
Farnaz Zahedifard (344791)
Shima Safaiyan (344792)
Elham Gholami (344793)
Fatemeh Doustdari (344794)
Kayhan Azadmanesh (344795)
Maryam Mirzaei (344796)
Nasir Saeedi Eslami (344797)
Akbar Khadem Sadegh (344798)
Ali Eslami far (344799)
Iraj Sharifi (344800)
Sima Rafati (344801)

Publication date

February 2013

DOI

10.1371/journal.pntd.0001295.t003

Abstract

<p>*strong binder (Strong binders have an IC<sub>50</sub> less than 50 nM).</p><p>**weak binder (Weak binders have an IC<sub>50</sub> more than 50 nM and less than 500 nM.</p

Extracted data

Related items

HLA-A*0201 binding of predicted HLA-A*0201 binders.

Nadia Caccamo (297600)
Giuliana Guggino (145109)
Serena Meraviglia (297590)
Giuseppe Gelsomino (372758)
Paola Di Carlo (372759)
Lucina Titone (372760)
Marialuisa Bocchino (359684)
Domenico Galati (372761)
Alessandro Matarese (372762)
Jan Nouta (372763)
Michel R. Klein (160302)
Alfredo Salerno (372765)
Alessandro Sanduzzi (359688)
Francesco Dieli (70261)
Tom H. M. Ottenhoff (160303)

February 2013

<p>Peptides were tested for their ability to compete binding of 1.6 µM biotinylated peptide HBV core...

Predicting the binding affinity of MHC class II peptides

Fatih Altiparmak
Altuna Akalin
Hakan Ferhatosmanoglu

January 2006

MHC (Major Histocompatibility Complex) proteins are categorized under the heterodimeric integral mem...

Sequence motifs important for peptide binding to the human MHC class I molecule HLA-A*0201and cA1 peptide structure using SYFPEITHI database.<sup>a</sup>

Ammar Achour (82007)
Jean-Michel Biquard (82008)
Velibor Krsmanovic (82009)
Jean-Pierre M'Bika (82010)
Damien Ficheux (17029)
Marianna Sikorska (66629)
Alain J. Cozzone (82011)

February 2013

a<p>HLA-A2-binding peptides are 8–10 amino acid (aa) residues long, with a Leu at position 2 (P2), a...

Positional biases of predicted binders for 12 HLA supertypes.

Yohan Kim (49009)
Jonathan W. Yewdell (236662)
Alessandro Sette (19132)
Bjoern Peters (19131)

January 2013

<p>For each supertype, 9-mer peptide binding predictions were carried out and ratios of probability ...

Prediction of T-cell epitopes that can bind the most prevalent BoLA types.

Jerome Nyhalah Dinga (751197)
Mark Wamalwa (679106)
Dieudonné Lemuh Njimoh (751198)
Moses N. Njahira (222424)
Appolinaire Djikeng (41915)
Rob Skilton (751199)
Vincent Pryde Kehdingha Titanji (751200)
Roger Pellé (5663848)

June 2015

<p>A rank threshold below or equal to 0.5 shows the peptide binds strongly with the corresponding Bo...

Affinities of peptides to MHC-II alleles.

Mingjun Wang (141725)
Mette V. Larsen (258357)
Morten Nielsen (33408)
Mikkel Harndahl (78384)
Sune Justesen (49943)
Morten H. Dziegiel (364992)
Søren Buus (49944)
Sheila T. Tang (364993)
Ole Lund (26628)
Mogens H. Claesson (364994)

February 2013

<p>Note: peptides marked in bold are positive controls included in the assay; HA<sub>306–318</sub> i...

Peptide binding affinities for human MHC II proteins.

Regina S. Salvat (682343)
Andrew S. Parker (682344)
Yoonjoo Choi (364868)
Chris Bailey-Kellogg (682345)
Karl E. Griswold (228273)

January 2015

<p>IC<sub>50</sub> values are plotted as cognate wild type and variant pairs, where lower IC<sub>50<...

Predicted class II MHC occupancy for self-peptides derived from a single donor with multiple MHC alleles.

Cristina Maria Costantino (185933)
Eric Spooner (155228)
Hidde L. Ploegh (32525)
David A. Hafler (185936)

January 2012

<p>Peptides with both weak (<500 nM) and strong (<50 nM) predicted affinity are considered as positi...

HLA-I binding affinity of peptide length variants located in the CLIP region of the invariant chain.

Marvin M. van Luijn (168343)
Arjan A. van de Loosdrecht (104098)
Margit H. Lampen (168348)
Peter A. van Veelen (168353)
Adri Zevenbergen (168357)
Michel G. D. Kester (119811)
Arnoud H. de Ru (168363)
Gert J. Ossenkoppele (168366)
Thorbald van Hall (168371)
S. Marieke van Ham (116154)

April 2012

*<p>Peptide found with HLA-I elutions.</p>†<p>Amino acid (AA) position in the invariant chain protei...

A list of predicted HLA-A*02 binding peptides derived from SATB1.

Mingjun Wang (141725)
Bingnan Yin (306702)
Satoko Matsueda (306697)
Lijuan Deng (203371)
Ying Li (38224)
Wei Zhao (14321)
Jia Zou (306704)
Qingtian Li (306706)
Christopher Loo (306710)
Rong-Fu Wang (306711)
Helen Y. Wang (306712)

February 2013

<p>Note: <sup>a</sup> Predicted T(1/2) of disassociation in minutes;</p>b<p>and <sup>c</sup> Higher ...

Binding predictions forPPE68peptides 121–145, 124–137 and 127–136 to HLA-class I alleles using the prediction methods nHLAPred/Compred and ProPred-I.

Abu S. Mustafa (618185)

August 2014

a<p>The results are shown as no. of HLA-class I molecules predicted to bind/number of HLA-class I mo...

HLA-A2 peptides demonstrated high binding affinity towards MHC class I molecule.

San Jiun Chai (822102)
Yoke Yeow Yap (84839)
Yoke Ching Foo (822103)
Lee Fah Yap (735740)
Sathibalan Ponniah (621311)
Soo Hwang Teo (687198)
Sok Ching Cheong (279737)
Vyomesh Patel (29261)
Kue Peng Lim (621307)

November 2015

<p>All 6 HLA-A2-restricted peptides demonstrate higher binding affinities towards HLA-A2 molecules s...

Peptide binding affinity of biotinylated HLA-A*0201 versus non-biotinylated.

Christian Leisner (87236)
Nina Loeth (87237)
Kasper Lamberth (78383)
Sune Justesen (49943)
Christina Sylvester-Hvid (87238)
Esben G. Schmidt (87239)
Mogens Claesson (87240)
Soren Buus (83984)
Anette Stryhn (87241)

February 2013

<p>The peptide binding affinities of the biotinylated HLA-A*0201-HAT-BSP was compared to the standar...

Binding affinity in nanomols of the most frequent peptides that activated T-cells.

Andréa Barbosa de Melo (278363)
Eduardo J. M. Nascimento (200745)
Ulisses Braga-Neto (257210)
Rafael Dhalia (16862)
Ana Maria Silva (278364)
Mathias Oelke (278365)
Jonathan P. Schneck (259226)
John Sidney (19127)
Alessandro Sette (19132)
Silvia M. L. Montenegro (278368)
Ernesto T. A. Marques (255177)

January 2013

<p>Numbers in bold: values of IC<sub>50</sub> below the cutoff of 1000 nmol by which determine that ...

Human MHC-II-restricted epitopes predicted from the SIM2 long peptide using IEDB tool.

Haydn T. Kissick (545664)
Martin G. Sanda (192861)
Laura K. Dunn (545665)
Mohamed S. Arredouani (192866)

April 2014

<p>Only the top epitopes having the lowest percentile score and lowest IC50 are selected. One epitop...

HLA-A*0201 binding of predicted HLA-A*0201 binders.

Nadia Caccamo (297600)
Giuliana Guggino (145109)
Serena Meraviglia (297590)
Giuseppe Gelsomino (372758)
Paola Di Carlo (372759)
Lucina Titone (372760)
Marialuisa Bocchino (359684)
Domenico Galati (372761)
Alessandro Matarese (372762)
Jan Nouta (372763)
Michel R. Klein (160302)
Alfredo Salerno (372765)
Alessandro Sanduzzi (359688)
Francesco Dieli (70261)
Tom H. M. Ottenhoff (160303)

February 2013

<p>Peptides were tested for their ability to compete binding of 1.6 µM biotinylated peptide HBV core...

Predicting the binding affinity of MHC class II peptides

Fatih Altiparmak
Altuna Akalin
Hakan Ferhatosmanoglu

January 2006

MHC (Major Histocompatibility Complex) proteins are categorized under the heterodimeric integral mem...

Sequence motifs important for peptide binding to the human MHC class I molecule HLA-A*0201and cA1 peptide structure using SYFPEITHI database.<sup>a</sup>

Ammar Achour (82007)
Jean-Michel Biquard (82008)
Velibor Krsmanovic (82009)
Jean-Pierre M'Bika (82010)
Damien Ficheux (17029)
Marianna Sikorska (66629)
Alain J. Cozzone (82011)

February 2013

a<p>HLA-A2-binding peptides are 8–10 amino acid (aa) residues long, with a Leu at position 2 (P2), a...

Positional biases of predicted binders for 12 HLA supertypes.

Yohan Kim (49009)
Jonathan W. Yewdell (236662)
Alessandro Sette (19132)
Bjoern Peters (19131)

January 2013

<p>For each supertype, 9-mer peptide binding predictions were carried out and ratios of probability ...

Prediction of T-cell epitopes that can bind the most prevalent BoLA types.

Jerome Nyhalah Dinga (751197)
Mark Wamalwa (679106)
Dieudonné Lemuh Njimoh (751198)
Moses N. Njahira (222424)
Appolinaire Djikeng (41915)
Rob Skilton (751199)
Vincent Pryde Kehdingha Titanji (751200)
Roger Pellé (5663848)

June 2015

<p>A rank threshold below or equal to 0.5 shows the peptide binds strongly with the corresponding Bo...

Affinities of peptides to MHC-II alleles.

Mingjun Wang (141725)
Mette V. Larsen (258357)
Morten Nielsen (33408)
Mikkel Harndahl (78384)
Sune Justesen (49943)
Morten H. Dziegiel (364992)
Søren Buus (49944)
Sheila T. Tang (364993)
Ole Lund (26628)
Mogens H. Claesson (364994)

February 2013

<p>Note: peptides marked in bold are positive controls included in the assay; HA<sub>306–318</sub> i...

Peptide binding affinities for human MHC II proteins.

Regina S. Salvat (682343)
Andrew S. Parker (682344)
Yoonjoo Choi (364868)
Chris Bailey-Kellogg (682345)
Karl E. Griswold (228273)

January 2015

<p>IC<sub>50</sub> values are plotted as cognate wild type and variant pairs, where lower IC<sub>50<...

Predicted class II MHC occupancy for self-peptides derived from a single donor with multiple MHC alleles.

Cristina Maria Costantino (185933)
Eric Spooner (155228)
Hidde L. Ploegh (32525)
David A. Hafler (185936)

January 2012

<p>Peptides with both weak (<500 nM) and strong (<50 nM) predicted affinity are considered as positi...

HLA-I binding affinity of peptide length variants located in the CLIP region of the invariant chain.

Marvin M. van Luijn (168343)
Arjan A. van de Loosdrecht (104098)
Margit H. Lampen (168348)
Peter A. van Veelen (168353)
Adri Zevenbergen (168357)
Michel G. D. Kester (119811)
Arnoud H. de Ru (168363)
Gert J. Ossenkoppele (168366)
Thorbald van Hall (168371)
S. Marieke van Ham (116154)

April 2012

*<p>Peptide found with HLA-I elutions.</p>†<p>Amino acid (AA) position in the invariant chain protei...

A list of predicted HLA-A*02 binding peptides derived from SATB1.

Mingjun Wang (141725)
Bingnan Yin (306702)
Satoko Matsueda (306697)
Lijuan Deng (203371)
Ying Li (38224)
Wei Zhao (14321)
Jia Zou (306704)
Qingtian Li (306706)
Christopher Loo (306710)
Rong-Fu Wang (306711)
Helen Y. Wang (306712)

February 2013

<p>Note: <sup>a</sup> Predicted T(1/2) of disassociation in minutes;</p>b<p>and <sup>c</sup> Higher ...

Binding predictions forPPE68peptides 121–145, 124–137 and 127–136 to HLA-class I alleles using the prediction methods nHLAPred/Compred and ProPred-I.

Abu S. Mustafa (618185)

August 2014

a<p>The results are shown as no. of HLA-class I molecules predicted to bind/number of HLA-class I mo...

HLA-A2 peptides demonstrated high binding affinity towards MHC class I molecule.

San Jiun Chai (822102)
Yoke Yeow Yap (84839)
Yoke Ching Foo (822103)
Lee Fah Yap (735740)
Sathibalan Ponniah (621311)
Soo Hwang Teo (687198)
Sok Ching Cheong (279737)
Vyomesh Patel (29261)
Kue Peng Lim (621307)

November 2015

<p>All 6 HLA-A2-restricted peptides demonstrate higher binding affinities towards HLA-A2 molecules s...

Peptide binding affinity of biotinylated HLA-A*0201 versus non-biotinylated.

Christian Leisner (87236)
Nina Loeth (87237)
Kasper Lamberth (78383)
Sune Justesen (49943)
Christina Sylvester-Hvid (87238)
Esben G. Schmidt (87239)
Mogens Claesson (87240)
Soren Buus (83984)
Anette Stryhn (87241)

February 2013

<p>The peptide binding affinities of the biotinylated HLA-A*0201-HAT-BSP was compared to the standar...

Binding affinity in nanomols of the most frequent peptides that activated T-cells.

Andréa Barbosa de Melo (278363)
Eduardo J. M. Nascimento (200745)
Ulisses Braga-Neto (257210)
Rafael Dhalia (16862)
Ana Maria Silva (278364)
Mathias Oelke (278365)
Jonathan P. Schneck (259226)
John Sidney (19127)
Alessandro Sette (19132)
Silvia M. L. Montenegro (278368)
Ernesto T. A. Marques (255177)

January 2013

<p>Numbers in bold: values of IC<sub>50</sub> below the cutoff of 1000 nmol by which determine that ...

Human MHC-II-restricted epitopes predicted from the SIM2 long peptide using IEDB tool.

Haydn T. Kissick (545664)
Martin G. Sanda (192861)
Laura K. Dunn (545665)
Mohamed S. Arredouani (192866)

April 2014

<p>Only the top epitopes having the lowest percentile score and lowest IC50 are selected. One epitop...

HLA-A*0201 binding of predicted HLA-A*0201 binders.

Nadia Caccamo (297600)
Giuliana Guggino (145109)
Serena Meraviglia (297590)
Giuseppe Gelsomino (372758)
Paola Di Carlo (372759)
Lucina Titone (372760)
Marialuisa Bocchino (359684)
Domenico Galati (372761)
Alessandro Matarese (372762)
Jan Nouta (372763)
Michel R. Klein (160302)
Alfredo Salerno (372765)
Alessandro Sanduzzi (359688)
Francesco Dieli (70261)
Tom H. M. Ottenhoff (160303)

February 2013

<p>Peptides were tested for their ability to compete binding of 1.6 µM biotinylated peptide HBV core...

Predicting the binding affinity of MHC class II peptides

Fatih Altiparmak
Altuna Akalin
Hakan Ferhatosmanoglu

January 2006

MHC (Major Histocompatibility Complex) proteins are categorized under the heterodimeric integral mem...

Sequence motifs important for peptide binding to the human MHC class I molecule HLA-A*0201and cA1 peptide structure using SYFPEITHI database.<sup>a</sup>

Ammar Achour (82007)
Jean-Michel Biquard (82008)
Velibor Krsmanovic (82009)
Jean-Pierre M'Bika (82010)
Damien Ficheux (17029)
Marianna Sikorska (66629)
Alain J. Cozzone (82011)

February 2013

a<p>HLA-A2-binding peptides are 8–10 amino acid (aa) residues long, with a Leu at position 2 (P2), a...