PMID: 19128216Jan 9, 2009Paper

Evaluation of molecular docking using polynomial empirical scoring functions

Current Drug Targets
Raquel DiasWalter Filgueira de Azevedo

Abstract

Molecular docking simulations are of pivotal importance for analysis of protein-ligand interactions and also an essential resource for virtual-screening initiatives. In molecular docking simulations several possible docked structures are generated, which create an ensemble of structures representing binary complexes. Therefore, it is crucial to find the best solution for the simulation. One approach to this problem is to employ empirical scoring function to identify the best docked structure. It is expected that scoring functions show a descriptive funnel-shaped energy surface without many false minima to impair the efficiency of conformational sampling. We employed this methodology against a test set with 300 docked structures. Docking simulations of these ligands against enzyme binding pocket indicated a funnel-shaped behavior of the complexation for this system. This review compares a set of recently proposed polynomial empirical scoring functions, implemented in a program called POLSCORE, with two popular scoring function programs (XSCORE and DrugScore). Overall comparison indicated that POLSCORE works better to predict the correct docked position, for the ensemble of docked structures analyzed in the present work.

Citations

Jan 28, 2009·Journal of Molecular Modeling·Ivani PauliWalter Filgueira de Azevedo
Aug 12, 2009·Journal of Molecular Modeling·Fernando Berton ZanchiWalter Filgueira de Azevedo
Jun 24, 2010·Bioorganic & Medicinal Chemistry·Rodrigo G DucatiWalter F de Azevedo
Feb 24, 2010·Journal of Pharmacological and Toxicological Methods·Sandhya Kortagere, Sean Ekins
Mar 14, 2009·Biophysical Chemistry·Luis Fernando Saraiva Macedo TimmersWalter Filgueira de Azevedo
Sep 3, 2010·Journal of Computational Chemistry·Dariusz PlewczynskiKrzysztof Ginalski
Dec 7, 2018·Current Medicinal Chemistry·Maurício Boff de ÁvilaWalter Filgueira de Azevedo

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Current Drug Targets
Fernanda Canduri, Walter Filgueira de Azevedo
Current Drug Targets
Raquel Dias, Walter Filgueira de Azevedo
Current Drug Targets
Walter Filgueira de Azevedo, Raquel Dias
Current Drug Targets
Ivani PauliWalter Filgueira de Azevedo
Current Drug Targets
Rafael Andrade CaceresWalter Filgueira de Azevedo
© 2021 Meta ULC. All rights reserved