Principles of Docking_ An Overview of Docking Algorithms .pptx

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					BIL 511 – Nesnesel Tasarım ve Programlama




                                                       Aytun Onay
                                            Yasemin Seren Demiray
                                                 Samet Hiçsönmez

    PRINCIPLES OF DOCKING: AN OVERVIEW OF
    DOCKING ALGORITHMS
OVERVIEW
Ø Introduction

Ø Docking Algorithms

   Ø BiGGER: Predicting Protein Interactions
   Ø Prediction of Protein Complexes by an NMR
   Ø Scheduling of Receiving and Shipping Trucks in Cross-Docking
     Systems
   Ø ASPDock :Using Atomic Solvation Parameters Model
   Ø A fast protein-ligand docking algorithm
   Ø Protein-Protein Docking based on Best-First Search Algorithm
   Ø Efficient Combinatorial Library Docking Using Recursive Algorithm

Ø Conclusions

Ø References
INTRODUCTION

       Different types of molecular docking methods are used
    to study molecular recognition. Using known structures,
    molecular docking aims to predict the binding mode and
    binding affinity of a complex formed by two or more
    constituent molecules.

       One of the important type of molecular dockings is
    protein-ligand docking because of its applications in modern
    structure-based drug design for many diseases. Protein-
    protein interactions play important roles in many biological
    processes such as signal transduction, cell regulation, and
    other macromolecular assemblies.
INTRODUCTION


 In this paper, we review the followings for
 predicting protein interactions, structure
 prediction of protein complexes:
  docking algorithms,
  cross-docking system,
  best-first search,
  library docking,
  flexible ligand docking
DOCKING ALGORITHMS
       Due to the difficulties and economic cost of the
    experimental methods for determining the structures
    of complexes, computational methods such as
    molecular docking are desired for predicting putative
    binding modes and affinities.

       There are two main aspects of a docking
    algorithm; scoring or measuring the quality of any
    given docked complex, and searching for the highest
    scoring or a pool of high quality docking
    conformations.
DOCKING ALGORITHMS

       In addition to this, docking is a term used for
    computational schemes that attempt to find the best
    matching between two molecules: a receptor and a
    ligand. The molecular docking problem can be defined
    as follows: Given the atomic coordinates of two
    molecules, predict their correct bound association.

       Here we attempt to look back on what has been
    achieved and to suggest what might be tried in the next
    steps.
BIGGER: PREDICTING PROTEIN INTERACTIONS

       Soft docking is a computationally efficient and
    automated docking algorithm which can be used
    to predict the mode of binding between two
    proteins using the three dimensional structures of
    the unbound molecules.

       BiGGER (Bimolecular Complex Generation with
    Global Evaluation and Ranking) is a software
    package where the method is implemented.
BIGGER:     PREDICTING        PROTEIN      INTERACTIO

The docking procedure has two modules.
   First module is BoGIE (Boolean Geometric
   Interaction Evaluation), a grid-like search algorithm
   to generate a population of docked geometries with
   maximal surface matching and favorable
   intermolecular amino acid contacts.
  Second module is the putative binding modes
   which are evaluated according to a set of
   interaction terms.
PREDICTION OF PROTEIN COMPLEXES BY AN NMR

Protein–Protein Docking Problems (PPD
 problem) can be formulated as follows:
  The 3D structure of two proteins A and B forms a
   protein complex AB, the 3D structure of the
   complex AB is computed and a variant of the PPD
   problem where the input consists of the tertiary
   structures of A and B plus an unassigned
   experimental 1H-NMR spectrum of the protein
   complex AB.
PREDICTION OF PROTEIN COMPLEXES BY AN NMR



 One of the important results is that the use
 of NMR data can improve the reliability and
 accuracy of docking predictions, another is the
 new method still needs a more extensive
 validation with experimental data.
SCHEDULING OF RECEIVING AND SHIPPING TRUCKS IN CROSS-DOCKING SYSTEMS



       Cross-docking system is transferring items directly from
    receiving trucks to shipping trucks without being held in
    storage at warehouse. An imperialistic competitive algorithm
    (ICA) is developed to use in system.

      In addition to this, cross-docking system is used to
    handle high volume of items in a short time.

       As a result of this, cost reduces with decreasing
    inventory and efficiency improves by increasing customer
    responsiveness and better control of distribution operation.
ASPDOCK :USING ATOMIC SOLVATION PARAMETERS MODEL

        One of the most improved docking algorithms is based on Fast
    Fourier Transform (FFT) which are widely used and have made great
    success. Because they can search 6D space in a very fast way.

         Atomic Solvation Parameters (ASP) model is used to calculate
    the binding free energy of protein complexes. An FFT-based algorithm
    is studied to calculate ASP scores of protein complexes and develop
    an ASP-based protein-protein docking method (ASPDock).

       We have observed from the results of the ASPDock that it is
    more accurate and physical than the pure shape complementarily in
    describing the feature of protein docking.
A FAST PROTEIN-LIGAND DOCKING ALGORITHM


       At the present day, drug discovery is a
    contemporary issue to find improved drugs for human
    diseases. Working on hydrogen bond matching and
    surface shape complementarity, a fast docking
    algorithm (H-DOCK) was developed for this aim. The
    aim of the docking procedure in H-DOCK is to
    maximize the intermolecular hydrogen bonding and to
    avoid large steric hindrance between protein and
    ligand.
A FAST PROTEIN-LIGAND DOCKING ALGORITHM

The flowchart of the H-DOCK algorithm is
 below;
 
PROTEIN-PROTEIN DOCKING BASED ON BEST-FIRST SEARCH
ALGORITHM

 Protein-protein docking method developed
 based on Best-First search algorithm which is
 used for imitating protein-protein interactions.
 The method consists of two stages:
  The first stage is that performs a rigid search on
   the unbound proteins.
  Second stage is searching alternately on rigid and
   flexible degrees of freedom starting from multiple
   configurations from the rigid search.
EFFICIENT COMBINATORIAL LIBRARY DOCKING USING RECURS
ALGORITHM


        In this method how the structure of combinatorial
    libraries can be exploited to speed up docking
    predictions were studied using incremental construction
    method implemented in the docking software FLEXX.

       Because of the relating ligands within the dataset
    structurally, to be generated a minimal tree structure
    representing the whole ligand dataset and to be
    speeded up conformational searching based on
    clustering similar molecules. In both cases, the derived
    hierarchy of molecules can then be used in an
    incremental construction docking method.
CONCLUSIONS
       Because of the protein flexibility, which has only been
  addressed recently because of the difficulty resulting from the
  enormous degrees of freedom and the limitation of the
  computing power, computational molecular docking problem is
  far from being solved.
       Nevertheless, despite the drawbacks in each docking
  strategy, significant progress has been made. Algorithms have
  been remarkably successful especially in addressing the
  protein–protein docking problem.
       Computational generation of protein structures and the
  docking of modeled protein structures with potential interacting
  partners will have great impact on the life sciences.
REFERENCES
 Lin Li, Dachuan Guo, Yangyu Huang, Shiyong Liu, Yi Xiao, ASPDock: protein-protein docking
  algorithm., BMC Bioinformatics 2011.
 S. Forouharfard & M. Zandieh, An imperialist competitive algorithm to schedule of receiving., Int J Adv
  Manuf Technol (2010) 51:1179–1193.
 JAN FUHRMANN, ALEXANDER RURAINSKI, HANS-PETER LENHOF, DIRK NEUMANN, A New Lamarckian
  Genetic Algorithm., J Comput Chem 31: 1911–1918, 2010.
 EFRAT NOY, AMIRAM GOLDBLUM, Flexible Protein-Protein Docking Based on Best-First Search
  Algorithm, J Comput Chem 31: 1929–1943, 2010.
 Wenjia Luo & Jianfeng Pei & Yushan Zhu, A fast protein-ligand docking algorithm., J Mol Model (2010)
  16:903–913.
 Chun Hua Li, Xiao Hui Ma, Wei Zu Chen and Cun Xin Wang, A protein–protein docking algorithm.,
  Protein Engineering vol.16 no.4 pp.265–269, 2003.
 Oliver Kohlbacher, Andreas Burchardt, Andreas Moll, Andreas Hildebrandt, Peter Bayer& Hans-Peter
  Lenhof, Structure prediction of protein complexes by an NMR., Journal of Biomolecular NMR, 20: 15–
  21, 2001.
 MATTHIAS RAREY and THOMAS LENGAUER, A recursive algorithm for efficient combinatorial library
  docking, Perspectives in Drug Discovery and Design, 20: 63–81, 2000.
 JINN-MOON YANG, CHENG-YAN KAO, Flexible Ligand Docking., J Comput Chem 21: 988–998, 2000.
 P. Nuno Palma, Ludwig Krippahl, John E. Wampler, and Jose J.G. Moura, BiGGER: A New (Soft)
  Docking Algorithm., PROTEINS: Structure, Function, and Genetics 39:372–384 (2000).

				
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