Shape & Chemical Complementary Scores

فهرست عناوین اصلی در این پاورپوینت

فهرست عناوین اصلی در این پاورپوینت

● Molecular Docking
● Docking Challenge
● Two main tasks of Docking Tools
● Introducing flexibility:
Whole molecule docking
● Monte Carlo
● Molecular Dynamics
● Simulated Annealing
● Genetic Algorithms
● Introducing flexibility:
Fragment Based Methods
● Placing Fragments and Rigid Molecules
● Geometric hashing
● Pose-Clustering
● Clique-Detection
● Scoring Functions
● Shape & Chemical Complementary Scores
● Empirical Scoring
● Empirical scoring
● Force Field Scoring (Dock)
● Knowledge-based Scoring Function
● Potential of Mean Force (PMF)
● Consensus Scoring
● Virtual screening by Docking
● Concluding remarks
● Docking programs
● FLEXX
● How DOCK works

نوع زبان: انگلیسی حجم: 0.89 مگا بایت
نوع فایل: اسلاید پاورپوینت تعداد اسلایدها: 30 صفحه
سطح مطلب: نامشخص پسوند فایل: ppt
گروه موضوعی: زمان استخراج مطلب: 2019/06/15 12:27:12

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عبارات مهم استفاده شده در این مطلب

عبارات مهم استفاده شده در این مطلب

score, ., ligand, docking, force, energy, ij, atom, protein, r, interaction, rigid,

توجه: این مطلب در تاریخ 2019/06/15 12:27:12 به صورت خودکار از فضای وب آشکار توسط موتور جستجوی پاورپوینت جمع آوری شده است و در صورت اعلام عدم رضایت تهیه کننده ی آن، طبق قوانین سایت از روی وب گاه حذف خواهد شد. این مطلب از وب سایت زیر استخراج شده است و مسئولیت انتشار آن با منبع اصلی است.

https://swift.cmbi.umcn.nl/teach/SEMINARS/dock_sem.ppt

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عبارات پرتکرار و مهم در این اسلاید عبارتند از: score, ., ligand, docking, force, energy, ij, atom, protein, r, interaction, rigid,

مشاهده محتوای متنیِ این اسلاید ppt

مشاهده محتوای متنیِ این اسلاید ppt

molecular docking g. schaftenaar explain docking is fitting ligand into the receptor steric and electrostatic match docking challenge identification of the ligand’s correct binding geometry in the binding site binding mode observation similar ligands can bind at quite different orientations in the active site. two main tasks of docking tools sampling of conformational ligand space scoring protein ligand complexes historically the first approaches. protein and ligand fixed. search for the relative orientation of the two molecules with lowest energy. flog flexible ligands oriented on grid each ligand represented by up to ۲۵ low energy conformations. rigid body docking algorithms introducing flexibility whole molecule docking monte carlo methods mc molecular dynamics md simulated annealing sa genetic algorithms ga available in packages autodock mc ga sa gold ga sybyl md ga available in gold genetic optimisation for ligand docking md a force field is used to calculate the forces an each atom. following newton mechanics velocities and accelerations are calculated atoms are moved with respect to a time step mc local moves of atoms are performed randomly sa optimisation technique ۱ starting form conformation a with energy score ea ۲ calculate random local move to configuration b with eb ۳ accept on the basis of metropolis criterion a if eb is lower than ea b with probability p exp eb ea kt monte carlo start with configuration a energy ea make random move to configuration b energy eb accept move when eb ea or if eb ea except with probability p molecular dynamics force field is used to calculate forces on each atom of the simulated system following newton mechanics calculate accelerations velocities and new coordinates from the forces. force mass times acceleration the atoms are moved slightly with respect to a given time step simulated annealing finding a global minimium by lowering the temperature during the monte carlo md simulation genetic algorithms ligand translation rotation and configuration variables constitute the genes crossovers mixes ligand variables from parent configurations mutations randomly change variables natural selection of current generation based on fitness energy scoring function determines fitness introducing flexibility fragment based methods build small molecules inside defined binding sites while maximizing favorable contacts. de novo methods construct new molecules in the site. division into two major groups incremental construction flexx dock place join. the first group places a single fragment or seed in a binding cavity and in a stepwise manner other groups are attached to the growing structure. the second group of methods places key functional groups into a binding site and then attempts to connected these together into a single structure. grow ludi sprout placing fragments and rigid molecules all rigid body docking methods have in common that superposition of point sets is a fundamental sub problem that has to be solved efficiently geometric hashing pose clustering clique detection geometric hashing originates from computer vision given a picture of a scene and a set of objects within the picture both represented by points in ۲d space the goal is to recognize some of the models in the scene first applied to molecular docking program sby fischer norel nussinov wolfson ۱۹۹۳ cpm۹۳ ۲ ۳۴ and fischer lin wolfson and nussinov ۱۹۹۵ j. mol. biology ۲۴۸ ۴۵۹ ۴۷۷. pose clustering for each triangle of receptor compute the transformation to each ligand matching triangle. cluster transformations. score the results. clique detection nodes comprise of matches between protein and ligand edges connect distance compatible pairs of nodes in a clique all pair of nodes are connected rigid –body docking in the dock program scoring functions shape chemical complementary scores empirical scoring force field scoring knowledge based scoring consensus scoring shape chemical complementary scores divide accessible protein surface into zones hydrophobic hydrogen bond donating hydrogen bond accepting do the same for the ligand surface find ligand orientation with best complementarity score plp score piece wise lineair potential score ussually for rigid docking empirical scoring scoring parameters fit to reproduce measured binding affinities flexx ludi hammerhead empirical scoring loss of entropy during binding hydrogen bonding ionic interactions aromatic interactions hydrophobic interactions force field scoring dock å å ú ú ù ê ê ë é lig i prot j i ij ij ij ij nonbond r b r a e c ۶ ۱۲ nonbonding interactions ligand protein van der waals electrostatics amber force field knowledge based scoring function free energies of molecular interactions derived from structural information on protein ligand complexes contained in pdb boltzmann like statistics of interatomic contacts. example drugscore potentials of mean force distribution of interatomic distances is converted into energy functions by inverting boltzmann’s law. f p n o the distribution of interatomic distances is converted into energy functions by inverting boltzmann’s law. it is not boltzmann’s law that determines the distribution observed in the pdb in the first place. an ensemble of structural parameters obtained from chemically different compounds in different crystal structures does not even remotely resemble a closed system at thermal equilibrium assumption pair interaction are independent. potential of mean force pmf ÷ ÷ ø ö ç ç è æ ij seg i corr vol b ij r r f t k r f s ln r ij seg s number density of atom pairs of type ij at atom pair distance r number density of atom pairs of type ij in reference sphere with radius r consensus scoring cscore integrate multiple scoring functions to produce a consensus score that is more accurate than any single function for predicting binding affinity. virtual screening by docking find weak binders in pool of non binders many false positives ۹۶ ۱ consensus scoring reduces rate of false positives concluding remarks docking programs dock flexx gold autodock hammerhead flog flexx receptor is treated as rigid incremental construction algorithm break ligand up into rigid fragments dock fragments into pocket of receptor reassemble ligand from fragments in low energy conformations incremental construction ۱ adding next fragment in all possible conformations to all placements befor ۲ search for new protein ligand interactions ۳ optimising ligand position to improve interaction and reduce strain ۴ select a subset of placement with high score ۵ clustering of these placements bohm empirical scoring fit coefficients of physical contributions ludi flexx knowledge based scoring statistical preferences can be derived between protein and ligand that are similar to potentials of mean field force field or energy scoring speaks for itself dock score best for apolar flexx best for polar how dock works generate molecular surface of protein cavities in the receptor are used to define spheres blue the centres are potential locations for ligand atoms. thioketal in the hiv۱ protease active site sphere centres are matched to ligand …

کلمات کلیدی پرکاربرد در این اسلاید پاورپوینت: score, ., ligand, docking, force, energy, ij, atom, protein, r, interaction, rigid,

این فایل پاورپوینت شامل 30 اسلاید و به زبان انگلیسی و حجم آن 0.89 مگا بایت است. نوع قالب فایل ppt بوده که با این لینک قابل دانلود است. این مطلب برگرفته از سایت زیر است و مسئولیت انتشار آن با منبع اصلی می باشد که در تاریخ 2019/06/15 12:27:12 استخراج شده است.

https://swift.cmbi.umcn.nl/teach/SEMINARS/dock_sem.ppt

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