Posts Tagged ‘scoring function’

Aplicando os Modêlos da Matrix/DNA para Obter Resultados Lucrativos: Scoring Functions, Computer Simulations for Drugs Search

segunda-feira, dezembro 10th, 2012

Importantissimo novo canal aberto para a Matrix/DNA pesquisar e tentar obter resultados reais aqui e agora!

Tudo começou ao ler o seguinte debate:

detroitjames2012 1 hour ago

Creationism/ Intelligent Design is not the proof of the bible, or odin, or krisha, or anything else. It is the understanding of recognizing design when it is present. Physics allow for clay to self assemble into a statue of Einstein, but if I walk past a statue of Einstein I don’t say “there’s no proof it was intelligently designed. Physics clearly allow for it to happen on it’s own”. I don’t suspend belief in the same logic and reason that allow me to navigate reality because the topic is ID.

·in reply to icook1723(Show the comment)

icook1723 1 hour ago

Yes, and evolution computer algorithms clearly show that, “in theory” given a population of randomly replicating replicators and a non-random survival search input, you can achieve results that look like design.

I use such algorithms to generate protein-ligand models that are used as a basis of drug engineering. The program uses “randomness” to search the space of possible solutions to identify the best one. These models are subsequently validated by experimentation.

·in reply to detroitjames2012

TheMatrixDNA 1 second ago

That’s very good new information for my personal studies. Could you be more detailed, please? I know I must type yours words doing a Google search, but any direct link will save my time. If I understood it, the key of this method is the “non-random survival model”. How do you has detected the survival search model for molecules, as proteins?! By other hand, I think that Matrix/DNA model of perfect closed systems must be the survival model applied by atoms/molecules (thermodynamic equilibrium)

·in reply to icook1723(Show the comment)

detroitjames2012 48 minutes ago

Nobody is denying the existence of your computer or it’s power to process algorithms. I’m denying your claim of knowing the existence of ‘randomy replicating replicators’ without your consciousness, since randomly replicating replicators cannot randomly replicate resulting in any definable reality without an intervening consciousness to assert it. There would be merely a realm of ‘infinite everything that’s ever possible’ including the idea of randomness and replication.

·in reply to icook1723(Show the comment)

TheMatrixDNA 1 second ago

My friend! What happens when a first single cell, resulting from the fusion of spermatozoon and ovule, becomes a replicating replicator, making billions of copies, each one different from all others? What is the difference between this scene you can see here and now with the hypothetical scene calculated as abiogenesis, where the results of such replications are supposed to be randomly? But… how are you seeing a mother giraffe (previous design) applying consciousness for her ovule doing that?

icook1723 32 minutes ago

The input is a randomly generated initial population (100), a scoring function, and a mutation rate that will insert random mutations that are not present in the parents. The program then ranks generation zero, and the bottom 50 are “killed”, the top 50 are randomly mated to create 50 new solution. Novel mutants are inserted into these new solutions (3 per generation) and they are scored and ranked with the parents. Repeat this process 2500 generation, and you get clusters of possible solutions.

TheMatrixDNA 1 second ago

That’s great! Labs could save billions dollars, years time if discovers Matrix/DNA models. It is explained by an analogy. Aliens intelligence were observing an Islamic country, trying to understand the behavior, the forces driven those people as organized group. They had hard time because the matter of humans bodies are composed by atoms and cells which has different set of tendencies. Everything were finally explained when they knew about a book, Koran. The Matrix is the book driven proteins

·in reply to icook1723(Show the comment)

detroitjames2012 2 minutes ago

I don’t know how else to say it You have to zoom out. Zoom out so far that you aren’t even holding the damn camera anymore.

“Scoring functions”, “initial populations”, and the mere idea of “random” are definitions of a reality which cannot exist without a consciousness to determine the nature of such concepts.

The fact that you are creating ‘rules of the universe’ by allowing IDEAS even to exist inherently mean you are playing god by allowing your consciousness to determine definitions.

·in reply to icook1723(Show the comment)

detroitjames2012 45 minutes ago

… and if such a realm exists to hold the idea of ‘randomness’ and ‘replication’ in the absence of consciousness, it forces us to retreat to the perspective of viewing the ‘universe’ from a birds-eye view capable of understanding it in it’s entirety… what would that make us?

·in reply to icook1723(Show the comment)

TheMatrixDNA 2 seconds ago

Ok. Detroit is an observer seeing theoretically the relations between consciousness and its productions called “humans concepts”, as “randomness”, “replication”, “scoring functions”, etc. And Icook is an practical observer in a lab seeing proteins, “drugs”, etc. The debate has common denominators, they are the words: randomness, replication, initial population, etc. For Detroit the first cause is consciousness, for Icook, it is matter. Anyone could analyze the debate suggesting a solution?

Primeiro, saber o que é “scoring function”:

Scoring functions for docking

In the fields of computational chemistry and molecular modellingscoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent

(A noncovalent bond is a type of chemical bond, typically between macromolecules, that does not involve the sharing of pairs of electrons, but rather involves more dispersed variations of electromagnetic interactions. The noncovalent bond is the dominant type of bond between supermolecules in supermolecular chemistry.[1] Noncovalent bonds are critical in maintaining the three-dimensional structure of large molecules, such as proteins and nucleic acids, and are involved in many biological processes in which large molecules bind specifically but transiently to one another. The energy released in the formation of noncovalent bonds is on the order of 1-5 kcal per mol.[2] There are four commonly mentioned types of non-covalent interactions: hydrogen bondsionic bondsvan der Waals forces, and hydrophobic interactions.[2] The noncovalent interactions hold together the two strands of DNA in the double helix, stabilize secondary and tertiary structures of proteins, and enable enzymesubstrate binding and antibodyantigen association. Ver resto )

interaction (also referred to as binding affinity), between two molecules after they have been docked.

(In the field of molecular modelingdocking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.[1]Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions. Ver resto)

Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug’s biological target such as a protein receptor.[1] Scoring functions have also been developed to predict the strength of other types of intermolecular interactions, for example between two proteins[2] or between protein and DNA.[3]