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Literature DB >> 11170640

Improved scoring of ligand-protein interactions using OWFEG free energy grids.

Abstract

A new approach to rapidly score protein-ligand interactions is tested on several protein-ligand systems. Results using this approach - the OWFEG free energy grid - are quite promising and are generally in better agreement with experiment (in some cases much better) than those obtained employing scoring techniques currently in wide use. The OWFEG free energy grid is generated from a one-window free energy perturbation MD simulation (Pearlman, D. A. J. Med. Chem. 1999, 42, 4313-4324). The OWFEG approach is applied to three protein systems: IMPDH, MAP kinase p38, and HIV-1 aspartyl protease. OWFEG scores are compared to experimental K(i) and IC50 data in each case. Empirical scoring functions applied to the same systems for comparison include ChemScore, Piecewise Linear Potential (PLP), and Dock energy score.

Entities: Species

Mesh：

Substances：
Ligands
Proteins

Year: 2001 PMID： 11170640 DOI： 10.1021/jm000375v

Source DB: PubMed Journal: J Med Chem ISSN： 0022-2623 Impact factor: 7.446

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Cited

16 in total

1. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol.

Authors: Mari Gabrielsen; Rafał Kurczab; Aina W Ravna; Irina Kufareva; Ruben Abagyan; Zdzisław Chilmonczyk; Andrzej J Bojarski; Ingebrigt Sylte
Journal: Eur J Med Chem Date: 2011-10-20 Impact factor: 6.514

2. Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK.

Authors: Natalie B Vinh; Jamie S Simpson; Peter J Scammells; David K Chalmers
Journal: J Comput Aided Mol Des Date: 2012-04-20 Impact factor: 3.686

3. Surrogate docking: structure-based virtual screening at high throughput speed.

Authors: Sukjoon Yoon; Andrew Smellie; David Hartsough; Anton Filikov
Journal: J Comput Aided Mol Des Date: 2005-11-16 Impact factor: 3.686

4. Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures.

Authors: Kristin Tøndel; Endre Anderssen; Finn Drabløs
Journal: J Comput Aided Mol Des Date: 2006-05-02 Impact factor: 3.686

5. Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

Authors: Kuan-Wei Wu; Po-Chin Chen; Jun Wang; Ying-Chieh Sun
Journal: J Comput Aided Mol Des Date: 2012-09-18 Impact factor: 3.686

Improved scoring of ligand-protein interactions using OWFEG free energy grids.

1. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol.

2. Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK.

3. Surrogate docking: structure-based virtual screening at high throughput speed.

4. Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures.

5. Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

6. Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring.

7. The β2-adrenoceptor agonist formoterol stimulates mitochondrial biogenesis.

Review 8. Molecular dynamics: survey of methods for simulating the activity of proteins.

9. Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor.

10. FINDSITE: a threading-based approach to ligand homology modeling.