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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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