Small molecule binding site determined by the Sitemap analysis in three different IL-1R1 conformations extracted from the crystal structures.

Exhaustive comparison and classification of ligand-binding surfaces in proteins

Yoichi Murakami
Kengo Kinoshita
Akira R. Kinjo
Haruki Nakamura

August 2016

Abstract: Many proteins function by interacting with other small molecules (ligands). Identification...

1F1 epitope overlaps the receptor binding site.

Tshidi Tsibane (113683)
Damian C. Ekiert (113685)
Jens C. Krause (113687)
Osvaldo Martinez (113689)
James E. Crowe Jr. (113691)
Ian A. Wilson (113692)
Christopher F. Basler (113693)

December 2012

1F1 recognizes several residues involved in binding sialic acid receptors (red spheres). Addition...

Mathematical modeling and screening of ligand binding sites in protein using the tetrahedral motif method and double-centroid representation

Banerjee, Arkanjan

April 2012

A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express ...

Dscore values, volume sizes, hydrophilic and hydrophobic areas of the five binding sites in three IL-1R1 crystal structures (PDB entries: 4GAF, 1IRA and 1G0Y) identified by the Sitemap program.

Chao-Yie Yang (695092)

February 2015

Dscore values, volume sizes, hydrophilic and hydrophobic areas of the five binding sites in three...

Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

Chao-Yie Yang

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which...

Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

Chao-Yie Yang (695092)

February 2015

<div>The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor fami...

Dscore values, Volume sizes of up to five binding sites identified by the Sitemap program in 25 representative IL-1R1 conformations determined by the hierarchy cluster analysis of 1180 aMD generated conformations.

Chao-Yie Yang (695092)

February 2015

Binding sites with the Dscore value ≥ 0.83 are shown in bold font.Dscore values, Volume si...

RESEARCH ARTICLE Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

Chao-yie Yang

August 2016

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which...

Binding sites evaluation of the representative conformations of ST2ECD.

Chao-Yie Yang (695092)
James Delproposto (843775)
Krishnapriya Chinnaswamy (843776)
William Clay Brown (843777)
Shuying Wang (150543)
Jeanne A. Stuckey (632892)
Xinquan Wang (211905)

January 2016

(A) Dscore values and Site volumes detected in N1-N9 and M1-M8 where ...

Chemical structures of four compounds identified from in silico screening to the P2 site in conformation 289 and snapshots of the IL-1R1/ligand conformations at 2 ns of MD simulations.

Chao-Yie Yang (695092)

February 2015

L951, L1882, L1192 and L537 interact with IL-1R1 without significant deviations from their initia...

Structure—function analysis of human EL-la: identification of residues required for binding to the human type IIL-1 receptor

Emily Labriola-tompkins
Chitra Ch

September 2016

2To whom correspondence should be addressed Using oligonucleotide-directed mutagenesis, the binding ...

Developing a method to identify small molecule binding sites on proteins : a case study with ATP.

Li, Kun Quan.

January 2010

The binding of small molecule ligands onto proteins is a key step in many cellular processes. Depend...

Identification and analysis of ligand binding sites by computational mapping

Ngan, Chi Ho

January 2012

Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authori...

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Tanggis Bohnuud
Dima Kozakov
Or Vajda

August 2016

Many protein-protein interactions (PPIs) are compelling targets for drug discovery, and in a number ...

Druggble sites, mapping of conformations to PC1 and PC2 in conformations 289, 524, 496, and 903 and the small molecule hotspot at the P2 site of conformation 289.

Chao-Yie Yang (695092)

February 2015

(A-B), druggable sites (yellow points) in conformations 289, 524, 496, and 903 identified by the ...

Exhaustive comparison and classification of ligand-binding surfaces in proteins

Yoichi Murakami
Kengo Kinoshita
Akira R. Kinjo
Haruki Nakamura

August 2016

Abstract: Many proteins function by interacting with other small molecules (ligands). Identification...

1F1 epitope overlaps the receptor binding site.

Tshidi Tsibane (113683)
Damian C. Ekiert (113685)
Jens C. Krause (113687)
Osvaldo Martinez (113689)
James E. Crowe Jr. (113691)
Ian A. Wilson (113692)
Christopher F. Basler (113693)

December 2012

1F1 recognizes several residues involved in binding sialic acid receptors (red spheres). Addition...

Mathematical modeling and screening of ligand binding sites in protein using the tetrahedral motif method and double-centroid representation

Banerjee, Arkanjan

April 2012

A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express ...

Dscore values, volume sizes, hydrophilic and hydrophobic areas of the five binding sites in three IL-1R1 crystal structures (PDB entries: 4GAF, 1IRA and 1G0Y) identified by the Sitemap program.

Chao-Yie Yang (695092)

February 2015

Dscore values, volume sizes, hydrophilic and hydrophobic areas of the five binding sites in three...

Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

Chao-Yie Yang

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which...

Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

Chao-Yie Yang (695092)

February 2015

<div>The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor fami...

Dscore values, Volume sizes of up to five binding sites identified by the Sitemap program in 25 representative IL-1R1 conformations determined by the hierarchy cluster analysis of 1180 aMD generated conformations.

Chao-Yie Yang (695092)

February 2015

Binding sites with the Dscore value ≥ 0.83 are shown in bold font.Dscore values, Volume si...

RESEARCH ARTICLE Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

Chao-yie Yang

August 2016

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which...

Binding sites evaluation of the representative conformations of ST2ECD.

Chao-Yie Yang (695092)
James Delproposto (843775)
Krishnapriya Chinnaswamy (843776)
William Clay Brown (843777)
Shuying Wang (150543)
Jeanne A. Stuckey (632892)
Xinquan Wang (211905)

January 2016

(A) Dscore values and Site volumes detected in N1-N9 and M1-M8 where ...

Chemical structures of four compounds identified from in silico screening to the P2 site in conformation 289 and snapshots of the IL-1R1/ligand conformations at 2 ns of MD simulations.

Chao-Yie Yang (695092)

February 2015

L951, L1882, L1192 and L537 interact with IL-1R1 without significant deviations from their initia...

Structure—function analysis of human EL-la: identification of residues required for binding to the human type IIL-1 receptor

Emily Labriola-tompkins
Chitra Ch

September 2016

2To whom correspondence should be addressed Using oligonucleotide-directed mutagenesis, the binding ...

Developing a method to identify small molecule binding sites on proteins : a case study with ATP.

Li, Kun Quan.

January 2010

The binding of small molecule ligands onto proteins is a key step in many cellular processes. Depend...

Identification and analysis of ligand binding sites by computational mapping

Ngan, Chi Ho

January 2012

Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authori...

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Tanggis Bohnuud
Dima Kozakov
Or Vajda

August 2016

Many protein-protein interactions (PPIs) are compelling targets for drug discovery, and in a number ...

Druggble sites, mapping of conformations to PC1 and PC2 in conformations 289, 524, 496, and 903 and the small molecule hotspot at the P2 site of conformation 289.

Chao-Yie Yang (695092)

February 2015

(A-B), druggable sites (yellow points) in conformations 289, 524, 496, and 903 identified by the ...

Exhaustive comparison and classification of ligand-binding surfaces in proteins

Yoichi Murakami
Kengo Kinoshita
Akira R. Kinjo
Haruki Nakamura

August 2016

Abstract: Many proteins function by interacting with other small molecules (ligands). Identification...

1F1 epitope overlaps the receptor binding site.

Tshidi Tsibane (113683)
Damian C. Ekiert (113685)
Jens C. Krause (113687)
Osvaldo Martinez (113689)
James E. Crowe Jr. (113691)
Ian A. Wilson (113692)
Christopher F. Basler (113693)

December 2012

1F1 recognizes several residues involved in binding sialic acid receptors (red spheres). Addition...

Mathematical modeling and screening of ligand binding sites in protein using the tetrahedral motif method and double-centroid representation

Banerjee, Arkanjan

April 2012

A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express ...

Small molecule binding site determined by the Sitemap analysis in three different IL-1R1 conformations extracted from the crystal structures.

Abstract

Extracted data

Small molecule binding site determined by the Sitemap analysis in three different IL-1R1 conformations extracted from the crystal structures.

Abstract

Extracted data

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