The Comparison of Docking Search Algorithms and Scoring Functions

2016 ◽  
pp. 99-127 ◽  
Author(s):  
Marjana Novič ◽  
Tjaša Tibaut ◽  
Marko Anderluh ◽  
Jure Borišek ◽  
Tihomir Tomašič
Keyword(s):  
Organic Chemistry ◽  
Molecular Docking ◽  
Case Studies ◽  
Experimental Work ◽  
Cathepsin K ◽  
Docking Studies ◽  
Search Algorithms ◽  
Scoring Functions ◽  
Basic Information

This chapter, composed of two parts, firstly provides molecular docking overview and secondly two molecular docking case studies are described. In overview, basic information about molecular docking are presented such as description of search algorithms and scoring functions applied in various docking programs. Brief description of methods utilized in some of the most popular docking programs also applied in our experimental work is provided. AutoDock, CDOCKER, GOLD, FlexX and FRED were used for docking studies of the DC-SIGN protein, while GOLD was further used for docking studies of cathepsin K protein. Methods and results of our studies with their contribution to science and medicine are presented. Content of the chapter is therefore appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs.

scholarly journals The Comparison of Docking Search Algorithms and Scoring Functions

2017 ◽  
pp. 820-849
Author(s):  
Marjana Novič ◽  
Tjaša Tibaut ◽  
Marko Anderluh ◽  
Jure Borišek ◽  
Tihomir Tomašič
Keyword(s):  
Organic Chemistry ◽  
Molecular Docking ◽  
Case Studies ◽  
Experimental Work ◽  
Cathepsin K ◽  
Docking Studies ◽  
Search Algorithms ◽  
Scoring Functions ◽  
Basic Information

This chapter, composed of two parts, firstly provides molecular docking overview and secondly two molecular docking case studies are described. In overview, basic information about molecular docking are presented such as description of search algorithms and scoring functions applied in various docking programs. Brief description of methods utilized in some of the most popular docking programs also applied in our experimental work is provided. AutoDock, CDOCKER, GOLD, FlexX and FRED were used for docking studies of the DC-SIGN protein, while GOLD was further used for docking studies of cathepsin K protein. Methods and results of our studies with their contribution to science and medicine are presented. Content of the chapter is therefore appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs.

Molecular Docking at a Glance

2016 ◽  
pp. 1-38
Author(s):  
Maryam Hamzeh-Mivehroud ◽  
Babak Sokouti ◽  
Siavoush Dastmalchi
Keyword(s):  
Molecular Docking ◽  
Case Studies ◽  
Scientific Community ◽  
Docking Studies ◽  
Search Algorithms ◽  
Steady Increase ◽  
Scoring Functions ◽  
Exponential Expansion ◽  
And Performance ◽  
Computational Resources

The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.

Molecular Docking at a Glance

Oncology ◽  
2017 ◽  
pp. 764-803
Author(s):  
Maryam Hamzeh-Mivehroud ◽  
Babak Sokouti ◽  
Siavoush Dastmalchi
Keyword(s):  
Molecular Docking ◽  
Case Studies ◽  
Scientific Community ◽  
Docking Studies ◽  
Search Algorithms ◽  
Steady Increase ◽  
Scoring Functions ◽  
Exponential Expansion ◽  
And Performance ◽  
Computational Resources

The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.

Protein-Ligand Docking Methodologies and Its Application in Drug Discovery

2016 ◽  
pp. 196-219
Author(s):  
Sanchaita Rajkhowa ◽  
Ramesh C. Deka
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Drug Design ◽  
High Throughput Screening ◽  
Docking Studies ◽  
Stable Complex ◽  
Scoring Functions ◽  
Binding Modes ◽  
Structure Based Drug Design ◽  
Modern Drug

Molecular docking is a key tool in structural biology and computer-assisted drug design. Molecular docking is a method which predicts the preferred orientation of a ligand when bound in an active site to form a stable complex. It is the most common method used as a structure-based drug design. Here, the authors intend to discuss the various types of docking methods and their development and applications in modern drug discovery. The important basic theories such as sampling algorithm and scoring functions have been discussed briefly. The performances of the different available docking software have also been discussed. This chapter also includes some application examples of docking studies in modern drug discovery such as targeted drug delivery using carbon nanotubes, docking of nucleic acids to find the binding modes and a comparative study between high-throughput screening and structure-based virtual screening.

Recent Advancements in Docking Methodologies

Oncology ◽  
2017 ◽  
pp. 848-875
Author(s):  
Vijay Kumar Srivastav ◽  
Vineet Singh ◽  
Meena Tiwari
Keyword(s):  
Molecular Docking ◽  
Binding Free Energy ◽  
Binding Mode ◽  
Docking Studies ◽  
Protein Docking ◽  
Scoring Functions ◽  
Discovery Process ◽  
Ligand Complex ◽  
Small Molecule Databases ◽  
Homology Models

Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.

Identification of novel cathepsin K inhibitors using ligand-based virtual screening and structure-based docking

RSC Advances ◽  
2016 ◽  
Vol 6 (86) ◽  
pp. 82961-82968 ◽  
Author(s):  
Yali Wang ◽  
Ruolan Li ◽  
Zhihui Zheng ◽  
Hong Yi ◽  
Zhuorong Li
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Cathepsin K ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Cathepsin K Inhibitors

Compound 21 was identified as a cathepsin K (Cat K) inhibitor through pharmacophore virtual screening and molecular docking studies.

Protein-Ligand Docking Methodologies and Its Application in Drug Discovery

Oncology ◽  
2017 ◽  
pp. 891-914
Author(s):  
Sanchaita Rajkhowa ◽  
Ramesh C. Deka
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Drug Design ◽  
High Throughput Screening ◽  
Docking Studies ◽  
Stable Complex ◽  
Scoring Functions ◽  
Binding Modes ◽  
Structure Based Drug Design ◽  
Modern Drug

Molecular docking is a key tool in structural biology and computer-assisted drug design. Molecular docking is a method which predicts the preferred orientation of a ligand when bound in an active site to form a stable complex. It is the most common method used as a structure-based drug design. Here, the authors intend to discuss the various types of docking methods and their development and applications in modern drug discovery. The important basic theories such as sampling algorithm and scoring functions have been discussed briefly. The performances of the different available docking software have also been discussed. This chapter also includes some application examples of docking studies in modern drug discovery such as targeted drug delivery using carbon nanotubes, docking of nucleic acids to find the binding modes and a comparative study between high-throughput screening and structure-based virtual screening.

scholarly journals The Docking Studies of New Derivatives of N-Phenylanthranilic Acids as Inhibitors of Microsomal Prostaglandin E Synthase-1 (mPGES-1)

2018 ◽  
Author(s):  
Marharyta M. Suleiman ◽  
Diana A. Alferova ◽  
Valentina V. Druhovina ◽  
Olena M. Sergienko ◽  
Natalya P. Kobzar ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Studies ◽  
Prostaglandin E ◽  
Scoring Functions ◽  
Operating Environment ◽  
Prostaglandin E Synthase ◽  
Thermodynamic Probability ◽  
Derivatives Of ◽  
Microsomal Prostaglandin E Synthase

The aim of the study was to determine the possibility of suppression of the prostaglandin synthesis by new derivatives of N-phenylanthranilic acids; they inhibit the activity of the microsomal prostaglandin E synthase-1 (mPGES-1) enzyme using the method of a flexible molecular docking. For the docking studies the crystallographic structural models with high resolution from Protein Data Bank were used: mPGES-1 in the complex with glutathione (pdb code 4AL0). A flexible molecular docking was carried out using the Molecular Operating Environment (MOE) software package. According to the results of the docking studies four scoring functions were calculated (Affinity dG Scoring, Alpha HB Scoring, London dG Scoring, GBVI/WSA dG Scoring). The values of the scoring functions calculated indicate the thermodynamic probability and energy favorability of forming complexes between molecules of the substances under research and the specified receptor, in which arrangement of ligands in the active site of the receptor and residues of amino acids of side chains are of similar geometry and types of binding of the known inhibitors of mPGES-1 determined on the basis of the crystallographic studies.

Recent Advancements in Docking Methodologies

2016 ◽  
pp. 267-294
Author(s):  
Vijay Kumar Srivastav ◽  
Vineet Singh ◽  
Meena Tiwari
Keyword(s):  
Molecular Docking ◽  
Binding Free Energy ◽  
Binding Mode ◽  
Docking Studies ◽  
Protein Docking ◽  
Scoring Functions ◽  
Discovery Process ◽  
Ligand Complex ◽  
Small Molecule Databases ◽  
Homology Models

Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.

Sign in / Sign up

Export Citation Format

Share Document