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Dockres: a computer program that analyzes the output of virtual screening of small molecules.

Mezei M, Zhou MM - Source Code Biol Med (2010)

Bottom Line: This paper describes a computer program named Dockres that is designed to analyze and summarize results of virtual screening of small molecules.Analysis of virtual screening by Dockres led to both active and selective lead compounds.Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, New York 10029, USA. Mihaly.Mezei@mssm.edu.

ABSTRACT

Background: This paper describes a computer program named Dockres that is designed to analyze and summarize results of virtual screening of small molecules. The program is supplemented with utilities that support the screening process. Foremost among these utilities are scripts that run the virtual screening of a chemical library on a large number of processors in parallel.

Methods: Dockres and some of its supporting utilities are written Fortran-77; other utilities are written as C-shell scripts. They support the parallel execution of the screening. The current implementation of the program handles virtual screening with Autodock-3 and Autodock-4, but can be extended to work with the output of other programs.

Results: Analysis of virtual screening by Dockres led to both active and selective lead compounds.

Conclusions: Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere.

No MeSH data available.


Distribution of scores of the poses closest to residues 101-150 of uPAR/α5β1. The symbol * represents the highest occurrence, the digits 0-9 give the occurrence normalized on a 0-10 scale (* representing 10).
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Figure 3: Distribution of scores of the poses closest to residues 101-150 of uPAR/α5β1. The symbol * represents the highest occurrence, the digits 0-9 give the occurrence normalized on a 0-10 scale (* representing 10).

Mentions: Dockres can characterize an ensemble of poses in several ways. (1) A histogram can be prepared to show distribution of a number of poses found to be closest to each residue in the macromolecule - the distance between a ligand and a residue is obtained as the shortest distance between any ligand-residue atom pair. One example is shown in Figure 2, which illustrates the distribution for residues 101-150 of the protein uPAR/α5β1 [6]. (2) For each residue distribution of scores of the poses that are closest to it is also calculated. Figure 3 shows the score distribution plot corresponding to the same set of resides depicted in Figure 2. (3) Optionally, one can print RMSDs between different poses of the same ligand (if any) in the top-scoring list. Finally, (4) the overall number of poses with scores falling in 1 kcal/mol bins (starting from the highest score) is printed, which may be helpful to decide on what number of top-scoring poses to extract.


Dockres: a computer program that analyzes the output of virtual screening of small molecules.

Mezei M, Zhou MM - Source Code Biol Med (2010)

Distribution of scores of the poses closest to residues 101-150 of uPAR/α5β1. The symbol * represents the highest occurrence, the digits 0-9 give the occurrence normalized on a 0-10 scale (* representing 10).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823743&req=5

Figure 3: Distribution of scores of the poses closest to residues 101-150 of uPAR/α5β1. The symbol * represents the highest occurrence, the digits 0-9 give the occurrence normalized on a 0-10 scale (* representing 10).
Mentions: Dockres can characterize an ensemble of poses in several ways. (1) A histogram can be prepared to show distribution of a number of poses found to be closest to each residue in the macromolecule - the distance between a ligand and a residue is obtained as the shortest distance between any ligand-residue atom pair. One example is shown in Figure 2, which illustrates the distribution for residues 101-150 of the protein uPAR/α5β1 [6]. (2) For each residue distribution of scores of the poses that are closest to it is also calculated. Figure 3 shows the score distribution plot corresponding to the same set of resides depicted in Figure 2. (3) Optionally, one can print RMSDs between different poses of the same ligand (if any) in the top-scoring list. Finally, (4) the overall number of poses with scores falling in 1 kcal/mol bins (starting from the highest score) is printed, which may be helpful to decide on what number of top-scoring poses to extract.

Bottom Line: This paper describes a computer program named Dockres that is designed to analyze and summarize results of virtual screening of small molecules.Analysis of virtual screening by Dockres led to both active and selective lead compounds.Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, New York 10029, USA. Mihaly.Mezei@mssm.edu.

ABSTRACT

Background: This paper describes a computer program named Dockres that is designed to analyze and summarize results of virtual screening of small molecules. The program is supplemented with utilities that support the screening process. Foremost among these utilities are scripts that run the virtual screening of a chemical library on a large number of processors in parallel.

Methods: Dockres and some of its supporting utilities are written Fortran-77; other utilities are written as C-shell scripts. They support the parallel execution of the screening. The current implementation of the program handles virtual screening with Autodock-3 and Autodock-4, but can be extended to work with the output of other programs.

Results: Analysis of virtual screening by Dockres led to both active and selective lead compounds.

Conclusions: Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere.

No MeSH data available.