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Ligands protein

All the long-range forces discussed in this chapter play a role in biological processes. Interactions between membranes, proteins, ligands, antibodies... [Pg.246]

Bdhm H-J 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comp.-Aided Mol. Design 8 243-56... [Pg.2850]

The avidin-biotin complex, known for its extremely high affinity (Green, 1975), has been studied experimentally more extensively than most other protein-ligand systems. The adhesion forces between avidin and biotin have been measured directly by AFM experiments (Florin et al., 1994 Moy et al., 1994b Moy et al., 1994a). SMD simulations were performed on the entire tetramer of avidin with four biotins bound to investigate the microscopic detail of nnbinding of biotin from avidin (Izrailev et al., 1997). [Pg.43]

That simulation study [49] aimed at a microscopic interpretation of single molecule atomic force microscope (AFM) experiments [50], in which unbinding forces between individual protein-ligand complexes have been m( asured... [Pg.84]

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. [Pg.86]

Equilibria in Solution The stability of a protein-ligand complex in solution is measured in terms of the equilibrium constant and the standard free energy of association based on it. For association of species P and L in solution to form a complex PL, i.e., for... [Pg.130]

Simulation Studies of Protein-Ligand Interactions 141 Table 2. Table Ligand-protein interaction energies and free energies (kcal/mol). [Pg.141]

Bonaccorsi ct al. [204 defined for the first time the molecular electrostatic potential (MEP), wdicli is dearly tfie most important and most used property (Figure 2-125c. The clcctro.static potential helps to identify molecular regions that arc significant for the reactivity of compounds. Furthermore, the MEP is decisive for the formation of protein-ligand complexes. Detailed information is given in Ref [205]. [Pg.136]

R E and S L Bender 1997. Recognition of Protein-Ligand Complexes Applications to Drug sign. Chemical Reviews 97 1359-1472. [Pg.736]

I-J 1994. The Development of a Simple Empirical Scoring Fimction to Estimate the Binding istant for a Protein-ligand Complex of Known Three-Dimensional Structure. Journal of nputer-Aided Molecular Design 8 243-256. [Pg.736]

H-J 1998. Prediction of Binding Constants of Protein Ligands A Fast Method for the aritisation of Hits Obtained from De Novo Design or 3D Database Search Programs. Journal of nputer-Aided Molecular Design 12 309-323. [Pg.736]

I-J and G Klebe 1996. What Can We Learn From Molecular Recognition in Protein-Ligand nplexes for the Design of New Drugs Angewandte Chemie Iniemational Edition in English 2588-2614. [Pg.736]

Kramer B, M Rarey and T Lengauer 1999. Evaluation of the FLEXX Incremental Constructioi Algorithm for Protein-Ligand Docking. Proteins Structure, Function and Genetics 37 228-241. [Pg.739]

Orstan, A. Wojcik, J. F. Spectroscopic Determination of Protein-Ligand Binding Constants, /. Chem. Educ. 1987, 64, 814-816. [Pg.448]

This experiment provides a nice example of the application of spectroscopy to biochemistry. After presenting the basic theory for the spectroscopic treatment of protein-ligand interactions, a procedure for characterizing the binding of methyl orange to bovine serum albumin is described. [Pg.448]


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See also in sourсe #XX -- [ Pg.4029 ]

See also in sourсe #XX -- [ Pg.455 , Pg.505 ]




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A Practice Tutorial for Protein-Ligand Fingerprint Generation

Absolute Protein-Ligand Binding Constants

Activation of Polysaccharides for Covalently Attaching Ligands and Proteins

Affinity chromatography protein-ligand combinations

Affinity ligands for proteins

Affinity ligands, proteinic

Analyzing Protein-Ligand Interactions Using Pharmacophore Fingerprints

Assessment of Ligand and Protein Criteria

Automated ligand-protein docking

Automated ligand-protein docking applications

Automated ligand-protein docking prediction

Basic Thermodynamics of Protein-Ligand Interactions

Binding free energy protein-ligand interactions

Bio-molecular simulation protein-ligand interactions

Bioinformatics protein-ligand interactions

Blue copper proteins axial ligand

Blue copper proteins ligands, amino acid sequence

Carbohydrate-binding proteins ligands

Cell cycle protein modulation ligand receptor binding

Chemical descriptors protein-ligand interface

Chemical microarrays for studying protein-ligand interactions

Computational protein-ligand

Computational protein-ligand docking techniques

Contributions to Protein-Ligand Interactions

Crystallographic protein-ligand complexes

Cucumber basic blue protein ligands

Database ligand-protein complex

Databases Ligand-protein

Density functional theory protein-ligand interactions

Determination of standard uncertainties for protein-ligand contacts

Effect of ligands and other protein modifiers

Energetics of Ligand Binding to Proteins

Entropic effects, ligand-protein

Entropic effects, ligand-protein interaction

Enzymes and ligand-binding proteins

Experimental Approaches to Determine the Thermodynamics of Protein-Ligand Interactions

Fast Radical Footprinting for Protein-Ligand Interaction Analysis

Fingerprints for ligands and proteins

Fingerprints for ligands and proteins (FLAP

Force fields protein-ligand interactions

Free ligand-protein interaction

G-protein-coupled receptors ligands

Hemoglobin ligand-protein interaction

High-quality ligand-protein complexes

Hydrogen Exchange Mass Spectrometry for the Analysis of Ligand Binding and Protein Aggregation

Hydrophobic ligands, protein-ligand binding

I 6 Hydrogen Bonds in Protein-Ligand Complexes

INDEX protein ligand, binding

Interactions, protein receptor-ligand

Intermolecular Forces in Protein-Ligand Interactions

Interpretation protein-ligand interaction

Iron-sulfur proteins ligand

Ligand affinity receptor protein, binding site

Ligand and Protein Conformational Change

Ligand binding G proteins

Ligand binding in protein crystal structures

Ligand binding protein preferences

Ligand binding, photonic proteins

Ligand binding, protein Macrocyclization

Ligand binding, protein enkephalins

Ligand cellular protein binding assays

Ligand protein receptors

Ligand protein stability

Ligand retinol-binding protein

Ligand-binding Pocket into proteins

Ligand-functionalized protein-containing

Ligand-protein Binding dynamics

Ligand-protein Docking simulations

Ligand-protein Thermodynamics

Ligand-protein binding molecular dynamics

Ligand-protein complexes, induction

Ligand-protein complexes, induction functional

Ligand-protein complexes, induction functionals

Ligand-protein contacts

Ligand-protein interactions hydroxylation

Ligand-protein pairs

Ligand-protein systems

Ligand-receptor-G protein

Ligands as Wrappers of Proteins in PDB Complexes Bioinformatics Evidence

Ligands protein purification

Lipophilic protein-ligand contact surface

Membrane proteins, ligand interactions

Methods for protein-ligand docking

Molecular Recognition in Biology: Models for Analysis of Protein-Ligand

Molecular modeling protein-ligand interactions

Molecular protein-ligand

Molecular protein-ligand shape similarity

Monte Carlo equilibrium simulations of ligand-protein thermodynamics

Myoglobin ligand-protein interaction

Oligonucleotides: Superspecific Ligand for Targeting Nucleic Acids and Proteins

On-bead screening, protein ligands materials

On-bead screening, protein ligands principles

Online ligand-protein databases

PLIMSTEX Results for CaM and Intermediate Protein-Ligand Binding Species

Physicochemical Basis of Protein-Ligand Recognition

Physicochemical protein-ligand recognition

Planet - Protein-ligand Association Network

Protein bivalent ligands

Protein denaturation, ligand effect

Protein hydrophobic ligands

Protein interactions with ligands

Protein kinases characterizing kinase-ligand

Protein kinases kinase - ligand interactions

Protein ligand complexes

Protein ligand equilibria

Protein-Ligand Affinity Measurements

Protein-Ligand Association

Protein-Ligand Dissociation Rate Measurement

Protein-Ligand Interactions Engineering

Protein-Ligand Interactions Revealing Biological Specificity

Protein-Ligand Interactions mutated

Protein-Ligand Interactions mutations

Protein-Ligand Interactions phenotype

Protein-Ligand Interactions: From Molecular Recognition to Drug Design

Protein-ligand binding

Protein-ligand binding affinity

Protein-ligand binding affinity target proteins

Protein-ligand binding amino-aromatic interactions

Protein-ligand binding interactions

Protein-ligand binding mediation

Protein-ligand binding oxygen-aromatic interactions

Protein-ligand complexes, binding mode

Protein-ligand complexes, molecular

Protein-ligand complexes, molecular recognition

Protein-ligand conformations

Protein-ligand docking

Protein-ligand docking affinity

Protein-ligand docking complexes

Protein-ligand docking computational

Protein-ligand docking programs

Protein-ligand docking software

Protein-ligand docking techniques

Protein-ligand engineering

Protein-ligand interaction

Protein-ligand interaction fingerprint

Protein-ligand interactions QSAR studies

Protein-ligand interactions advantages

Protein-ligand interactions affinity measurements

Protein-ligand interactions binding affinity

Protein-ligand interactions binding order

Protein-ligand interactions calmodulin binding

Protein-ligand interactions characterization

Protein-ligand interactions disadvantages

Protein-ligand interactions examples

Protein-ligand interactions reductase

Protein-ligand interactions scoring

Protein-ligand interactions targets

Protein-ligand interactions, energetics

Protein-ligand interactions, factors affecting

Protein-ligand interactions/complexes

Protein-ligand interface

Protein-ligand recognition

Protein-ligand scoring functions

Protein-ligand screening

Protein/ligand molar ratio

Proteins ligand-induced changes

Proteins ligand-induced conformational

Proteins protein—ligand complexes

Proteins stability ligand binding

Proteins, direct ligands, catalytic

Proteins, direct ligands, catalytic binding

Proteins, direct ligands, catalytic metal ions

Proteins, ligand binding thermodynamics

Radiolabeled proteins, ligand binding

Rapid Protein-Ligand Structure Determination

Relative Protein-Ligand Binding Constants

Scoring Functions for Protein-Ligand Recognition

Scoring protein-ligand complexes

Screening Protein-Ligand Interactions

Simultaneous Ligand and Protein Conformational Change

Strong protein-ligand interactions

Structure-based computational models of ligand-protein binding dynamics and molecular docking

Targeting Cell Membrane Proteins Ligand-Gated Ion Channels

Thermodynamics protein-ligand interactions

Three-dimensional protein-ligand complex

Unbound states, protein-ligand binding

Unfavorable protein-ligand interactions

Using Gel Filtration to Study Ligand-Protein Interactions

Viral coat protein ligands

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