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Protein Ligands, Protein-Ligand Interactions

Protein Ligands


Online available information resources about protein ligands and protein-ligand interactions.

Further information categories about related topics are listed in the navigation menu on the left side of these page.

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Lecture Notes, Tutorials

Ligand-Protein Interactions
Lecture notes - Format: PDF

Protein-Ligand Docking
… and protein-protein ligand Docking - Format: PDF

Protein-Ligand Docking
This module provides a high-level introduction to the field of protein-ligand docking

Protein-Ligand Docking
Lecture notes. GMD - Format: PDF

Protein-Ligand Docking Methods
Lecture notes - Format: PDF

Protein-Ligand Interactions
How do proteins interact with ligands? - Format: PDF

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Partial Information

Calculation of Protein-Ligand Binding Affinities
This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches - Format: PDF

Ligand Interaction Diagrams

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Data and Databases

Affinity Database For Protein-Ligand Complexes. Registration required. University of Marburg

Bimolecular Interaction Network Database

Binding MOAD
A subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding

A protein-ligand interaction database for drug discovery

Database of Interacting Proteins

Database of Interacting Proteins

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Software and Programs

GOLD Protein-Ligand Docking
GOLD is a program for calculating the docking modes of small molecules in protein binding sites and is provided as part of the GOLD Suite, a package of programs for structure visualisation and manipulation (Hermes), for protein-ligand docking (GOLD) and for post-processing (GoldMine) and visualisation of docking results

Program for automatically plotting protein-ligand interactions

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… is a project which uses Internet-connected computers to perform scientific calculations that aid in the creation of new and improved medicines. The project aims to help cure diseases such as Human Immunodeficiency Virus (HIV). Docking@Home is a collaboration between the University of Delaware, The Scripps Research Institute, and the University of California , Berkeley

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A first-principles approach to protein-ligand interaction
PhD thesis, 2009 - Format: PDF

Free Energy Calculations
… of protein-ligand complexes with computational molecular dynamics. Dissertation, 2008. University of Göttingen

Protein-Ligand Interactions
Protein-Ligand Interactions: Docking, Design and Protein Conformational Change. PhD thesis, 2002. Caltech - Format: PDF

QM/MM Docking and Simulations of FRET
Dissertation, 2005. University of Erlangen

Simulation Methods
High throughput simulation methods for protein ligand docking. Dissertation, 2003. TU Dortmund

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Protein Ligands, Protein-Ligand Interactions
Proteins, ligands, interactions, docking, basics, research, database
24.02.2012 00:00:00 [link check]
24.02.2012 [site update]

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Related Books and Scientific Literature: Protein Ligands:


Jack Kyte

Structure in Protein Chemistry

The second edition of Structure in Protein Chemistry showcases the latest developments and innovations in the field of protein structure analysis and prediction. The book begins by explaining how proteins are purified and describes methods for elucidating their sequences of amino acids and defining their posttranslational modifications. Comprehensive explanations of crystallography and of noncovalent forcesDLionic interactions, hydrogen bonding, and the hydrophobic effectDLact as a prelude to an exhaustive description of the atomic details of the structures of proteins. The resulting understanding of protein molecular structure forms the basis for discussions of the evolution of proteins, the symmetry of the oligomeric associations that produce them, and the chemical, mathematical, and physical basis of the techniques used to study their structures. The latter include image reconstruction, nuclear magnetic resonance spectroscopy, proton exchange, optical spectroscopy, electrophoresis, covalent cross-linking, chemical modification, immunochemistry, hydrodynamics, and the scattering of light, X-radiation, and neutrons. These procedures are applied to study the folding of polypeptides and the assembly of oligomers. Biological membranes and their proteins are also discussed. Structure in Protein Chemistry serves as a comprehensive textbook for advanced undergraduates and graduate students, as well as a useful reference for professionals.

Garland Science; 2006

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