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Literature DB >> 22212342

Limiting assumptions in structure-based design: binding entropy.

Abstract

In order to deal with the complexity of biological systems at the atomic level, limiting assumptions are often made which do not reflect the reality of the system under study. One example is the assumption that the entropy of binding of the macromolecule is not influenced significantly by the different ligands. Recent experimental data on ligands binding to HIV-1 protease challenge this assumption.

Entities: Chemical Disease Gene Mutation Species

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Year: 2012 PMID： 22212342 PMCID： PMC3542636 DOI： 10.1007/s10822-011-9494-1

Source DB: PubMed Journal: J Comput Aided Mol Des ISSN： 0920-654X Impact factor: 3.686

23 in total

Review 1. Distance measurements in the nanometer range by pulse EPR.

Authors: Gunnar Jeschke
Journal: Chemphyschem Date: 2002-11-15 Impact factor: 3.102

2. The determination of pair distance distributions by pulsed ESR using Tikhonov regularization.

Authors: Yun-Wei Chiang; Peter P Borbat; Jack H Freed
Journal: J Magn Reson Date: 2005-02 Impact factor: 2.229

3. Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy.

Authors: Vladimir Yu Torbeev; H Raghuraman; Kalyaneswar Mandal; Sanjib Senapati; Eduardo Perozo; Stephen B H Kent
Journal: J Am Chem Soc Date: 2009-01-28 Impact factor: 15.419

4. SKATE: a docking program that decouples systematic sampling from scoring.

Authors: Jianwen A Feng; Garland R Marshall
Journal: J Comput Chem Date: 2010-11-15 Impact factor: 3.376

5. Structural information from orientationally selective DEER spectroscopy.

Authors: J E Lovett; A M Bowen; C R Timmel; M W Jones; J R Dilworth; D Caprotti; S G Bell; L L Wong; J Harmer
Journal: Phys Chem Chem Phys Date: 2009-07-02 Impact factor: 3.676

6. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments.

Authors: Fangyu Ding; Melinda Layten; Carlos Simmerling
Journal: J Am Chem Soc Date: 2008-05-15 Impact factor: 15.419

7. Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization.

Authors: John E DeLorbe; John H Clements; Martin G Teresk; Aaron P Benfield; Hilary R Plake; Laura E Millspaugh; Stephen F Martin
Journal: J Am Chem Soc Date: 2009-11-25 Impact factor: 15.419

Limiting assumptions in structure-based design: binding entropy.

Review 1. Distance measurements in the nanometer range by pulse EPR.

2. The determination of pair distance distributions by pulsed ESR using Tikhonov regularization.

3. Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy.

4. SKATE: a docking program that decouples systematic sampling from scoring.

5. Structural information from orientationally selective DEER spectroscopy.

6. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments.

7. Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization.

8. Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions.

Review 9. Intrinsically disordered proteins in human diseases: introducing the D2 concept.

10. Long distance PELDOR measurements on the histone core particle.

1. Microscopic insights into the NMR relaxation-based protein conformational entropy meter.

2. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.

3. Limiting assumptions in molecular modeling: electrostatics.

4. Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.

5. Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing the Length of an Alkyl Chain.

Review 6. Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.