PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry

Liwei Li, Justin J. Dantzer, Jonathan Nowacki, Brian J. O'Callaghan, Samy Meroueh

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy-enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive hand-curated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor-ligand complexes. The dataset can be accessed through a web interface at http://www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.

Original languageEnglish
Pages (from-to)529-532
Number of pages4
JournalChemical Biology and Drug Design
Volume71
Issue number6
DOIs
StatePublished - Jun 2008

Fingerprint

Calorimetry
Titration
Thermodynamics
Entropy
Ligands
Enthalpy
Drug Design
Free energy
Specific heat
Hand
Hot Temperature
Datasets
Pharmaceutical Preparations
Experiments
Compensation and Redress

Keywords

  • Binding thermodynamics
  • Enthalpy-entropy compensation
  • Isothermal titration calorimetry
  • Protein-ligand interaction

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine

Cite this

PDBcal : A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry. / Li, Liwei; Dantzer, Justin J.; Nowacki, Jonathan; O'Callaghan, Brian J.; Meroueh, Samy.

In: Chemical Biology and Drug Design, Vol. 71, No. 6, 06.2008, p. 529-532.

Research output: Contribution to journalArticle

@article{783fa18b198d4381b89266355ff17e73,
title = "PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry",
abstract = "Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy-enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive hand-curated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor-ligand complexes. The dataset can be accessed through a web interface at http://www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.",
keywords = "Binding thermodynamics, Enthalpy-entropy compensation, Isothermal titration calorimetry, Protein-ligand interaction",
author = "Liwei Li and Dantzer, {Justin J.} and Jonathan Nowacki and O'Callaghan, {Brian J.} and Samy Meroueh",
year = "2008",
month = "6",
doi = "10.1111/j.1747-0285.2008.00661.x",
language = "English",
volume = "71",
pages = "529--532",
journal = "Chemical Biology and Drug Design",
issn = "1747-0277",
publisher = "Blackwell",
number = "6",

}

TY - JOUR

T1 - PDBcal

T2 - A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry

AU - Li, Liwei

AU - Dantzer, Justin J.

AU - Nowacki, Jonathan

AU - O'Callaghan, Brian J.

AU - Meroueh, Samy

PY - 2008/6

Y1 - 2008/6

N2 - Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy-enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive hand-curated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor-ligand complexes. The dataset can be accessed through a web interface at http://www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.

AB - Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy-enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive hand-curated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor-ligand complexes. The dataset can be accessed through a web interface at http://www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.

KW - Binding thermodynamics

KW - Enthalpy-entropy compensation

KW - Isothermal titration calorimetry

KW - Protein-ligand interaction

UR - http://www.scopus.com/inward/record.url?scp=43949128085&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=43949128085&partnerID=8YFLogxK

U2 - 10.1111/j.1747-0285.2008.00661.x

DO - 10.1111/j.1747-0285.2008.00661.x

M3 - Article

C2 - 18482338

AN - SCOPUS:43949128085

VL - 71

SP - 529

EP - 532

JO - Chemical Biology and Drug Design

JF - Chemical Biology and Drug Design

SN - 1747-0277

IS - 6

ER -