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Scoring function

FlexX uses a variant of the SCORE1 scoring function developed by Hans-Joachim Boehm for the de novo enzyme inhibitor design package LUDI. The scoring function has the following form:

Where f is a penalty function for deviations from ideal geometry for each kind of interaction, and f* is a function penalizing for lipophilic interactions deviating from an ideal separation distance.

Dock

Dock 1.0, first described in 1982 [8] , was the first automated receptor-ligand docking program. It was developed in the Department of Pharmacology at the University of California at San Francisco. Dock 4.0, the current version, was released in 1997 [9] .

Search technique

Like FlexX, Dock is driven by the geometry of the ligand and active site. The program approximates the shape of the binding cavity of the receptor with spheres. It then attempts to match the ligand to some subset of the centers of these spheres. Early versions used geometric hashing (see this module, covering local alignment methods ) to perform this matching, but more recent versions use bipartite graph matching (version 3.5) and single graph matching (version 4.0) for improved speed.

Scoring function

Dock offers three scoring functions. The first is based on an approximation to the Lennard-Jones potential (Van der Waals interactions). This essentially enforces geometric alignment and shape constraints. The second uses the program DELPHI to calculate the electrostatic potential of the complex.The third calculates the energy of the complex under the AMBER force field.

Flexible receptor docking

Introduction

As previously mentioned, docking entails determining not only the identity and three dimensional structure of the bound ligand, but also how the binding process affects the conformation of the receptor. This section will review the different receptor flexibility representations that have been proposed to study receptor conformational changes in the context of structure based drug design.

A central paradigm which was used in the development of the first docking programs was the lock-and-key model first described by Fischer [10] . In this model the three dimensional structure of the ligand and the receptor complement each other in the same way that a lock complements a key. However, further work confirmed that the lock-and-key model is not the most correct description for ligand binding. A more accurate view of this process was first presented by Koshland [11] in the induced fit model. In this model the three dimensional structure of the ligand and the receptor adapt to each other during the binding process. It is important to note that not only the structure of the ligand but also the structure of the receptor changes during the binding process. This occurs because the introduction of a ligand modifies the chemical and structural environment of the receptor. As a result, the unbound protein conformational substates, corresponding to the low energy regions of the protein energy landscape are likely to change. The induced fit model is supported by multiple observations in different proteins such as streptavidin, HIV-1 protease, DHFR, aldose reductase and many others.

Questions & Answers

more explanation on GDP
Isaac Reply
it is a country total out put of goods and services divided by the total population of the country.I think it can also be derived from the country labour force,,because it mostly depend on the labour force and the level of technology .
Tantoh
labour force and technological progress leads to greater production increases the GDP
Ahmed
What is economics?
Bubu Reply
by this time
Emmanuel
It is a social science that analyses production,distribution and consumption of goods and services
Emmanuel
A social science that study human behavior in relationship with decision making
Jessica
What are the typical patterns of GDP for a high-income economy like the United States in the long run and the short run?
mwangala Reply
What are the limitation and significant of macroeconomic
Usman Reply
explain the significance of concerpt of opportunity cost in planning
Mwanaid Reply
what is meant by the price elasticity of demand?
Martine Reply
when price of a commodity increase it's demand contracts , and whe the price of a commodity decreases it's demand expands so the degree of change in demand in response to change in own price of the commodity is called PED . Ed = percentage change in quantity demanded / percentage change in price
shaswat
What are the limitations of macroeconomic and their segnificant
Usman Reply
Discuss the role of competition in stimulating economic growth?
Daniel Reply
competition stimulate economic growth because in such types of economy,they is no monopoly power every supplier will want to produce to meet customers choice which brings about quality production and attract invested and customers into such economy
Koka
competition creates Monopoly because of economy of scale. it's not antithesis but different side of same coin
toko
competition result in high economic growth since every firm will intend to provide quality services and products to meet customers needs and requirements unlike in Monopoly situation where a firm just provide what it want to resulting in large stock piles of unwanted products ,ie inefficiency, howev
Mark
microeconomics study part of the economy but macroeconomic study the whole economy
Olokun Reply
studying the whole economy, solving the problem of the economy and building up the economy
Olokun
micro means small while macro means large
Olokun
standard of living is the footsteps of an economy because it plays important role for country to have crucial view about their budget ,import and export
Olokun
it will be differ because economic agent will only take their views on some part of household
Olokun
can opportunity cost be zero
OBED Reply
how many types of transportation do we have
Jacob
yes. when a customer's purchasing power is high, he may have d ability to purchase all he needs, dt makes opportunity cost zero
George
please can give more explanation on this question
OBED
what are the factors production
PETER Reply
Labour capital entrepreneurs
Leta
Land,capital, labour,and the entrepreneur
Tantoh
I will like to know use of calculus in economics
JHUMA Reply
do they use it in economics?
Pranav
I want to know if I should take calculus or statistics and probability my senior year of highschool
Yahir
yes for example in monopolistic competitive market..... TR=TC* & THIS CALCULATED BY CHANGING( DERIVATIVE LAW) MR =MC ** WILL BE THE FORMULA THAT USE.
Leta
please in which topic in economic is the question coming from.
Tantoh
from PCF in economics
Leta
why is unitary proportional to responsiveness
Etim Reply
any tip for igcse economics exam?pls
Stacey Reply
well
The
What is a market
Divine Reply
what are the variables that affect demand
Divine
what are the variables that affect demand
Divine
what are the variables that affect demand
Divine
what are the variables that affect demand
Divine
what are the variables that affect demand
Divine
price of the related goods 2 price of the given commodity 3 income of the consumer 4 taste and preference 5 expectation in the future price
John
pls the taste and preference
Nas
explain briefly
Nas
a consumer taste and preference commodity changes for a time the man becomes
John
sorry sorry
John
is when the price of a commodity becomes high and can't afford example Samsung instead of iPhone
John
consumers who have high intense for goods will purchase the goods even if the price of that commodity increases because he or she preferred that commodity.people will be prefer iphone as its price increase
Yussif
as usual bad taste of preference is when a consumer regrets from one commodity to another in terms of the price
John
thanks alot
Nas
you're welcome
John
#Preference; #Income #Test
Dereje
#price Of Commodity #Income #Taste #Preference
Dereje
#Market is The Place Where Buyers And Sellers Are Exchanging Their Goods And service. #
Dereje
difference between macro and micro economics
Lawrence
Microeconomic Study about individual consumers market But Macroeconomis Study General economic Process Such As #Aggregate Demand #Aggregate Supples #GDp= #GNp
Dereje
nice so can u run down a brife discussion on GDP
Lawrence
good
Chinex
Researchers demonstrated that the hippocampus functions in memory processing by creating lesions in the hippocampi of rats, which resulted in ________.
Mapo Reply
The formulation of new memories is sometimes called ________, and the process of bringing up old memories is called ________.
Mapo Reply
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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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