Posts by Venturini Dario[VENETO]

21) Message boards : Cafe Rosetta : Translating the video on Youtube (Message 51251) Posted 8 Feb 2008 by Venturini Dario[VENETO] Post: Ok I'll try another way. Thanks anyway
22) Message boards : Cafe Rosetta : Translating the video on Youtube (Message 51219) Posted 7 Feb 2008 by Venturini Dario[VENETO] Post: Me and my team (BOINC.Italy) have chosen to translate the video about Rosetta that is on Youtube http://www.youtube.com/watch?v=GzATbET3g54 to italian. We haven't decided yet if we will just put subtitles or a whole new audio. We will then host it on Youtube as a "response video" to yours. I've tried to write a transcription of the text but being not an english native speaker there are some words I didn't catch. It took me about 2 days to get this, which is the best I could. Could anyone correct my work? We will also put it at everyone's disposal in case someone else decides to translate it. "The problem we're focusing on, at Rosetta@Home, is the prediction of protein structures from their aminoacid sequences. Almost all human diseases are caused by mutations in proteins that affect their tridimensional structures and functions and so if we can reliably predict protein structures we could understand how mutations cause disease and from there perhaps go on to develop therapies. I'm working on trying to design immunogens that will XXX? antibodies against HIV so, critical part about a vaccine. Design proteins that will present that piece of HIV in just the right conformation so that protein, once it is taken off the computer and turned into a real phisical protein could be put into a person's XXX? and cause that person to make antibodies against the XXX? of HIV. Up until recently, it has been pretty much about impossible to reliably predict the structure of proteins from their sequences. Instead protein structures are XXXly? determined using time consuming and expensive experiments, which could only be applied to a small subset of proteins. If instead we could accurately and reliable predict protein structures, it will revolutionize much of molecular biology. To carry up this work, we've developed the computer program called Rosetta. Success in our work would have broad ranging applications for human's health ranging from development of a vaccine for HIV to the eradication of Malaria The sequence of amminoacids that make up proteins is directly determined from the genetic code, otherwise known as the sequence of molecules in DNA. DNA, like proteins, is also made of molecular sub-units with specific properties. WIthin the nucleus a kind of XXX? of DNA is transcribed into a similar molecule called RNA. Carrier molecules transport aminoacids to an enormous structure called the ribosome. The ribosome translates the information in RNA into a chain of aminoacids You know, think about putting a rope in a box of no gravity and think about how many different ways this rope could actually fall in that box. So you know the number of combination, the number of possibilities, are pretty much astronomical. A strand of aminoacids, the order of which has been determined by the genetic code, can indeed be thought of as warped or chain-like. However, the properties of the links, in this case aminoacids, cause portions of the chain to be attracted to or repelled from each other. As well as elements in the cellular environment. What the Rosetta program does, is calculate the likelihood of these interactions between segments of the chain, based upon favorable energy levels. The most likely 3D structure of the chain will take the least amount of free energy to fold. So last summer I started modifying Rosetta to be used with the BOINC distributed computing platform. Before BOINC we had about 400 computers that we can run our calculations on locally, but now with BOINC we have thousands of computers we can run our jobs on, located all around the globe, and it's really exciting to how it developed. What we're doing at Rosetta@Home, is analogous to searching the surface of a large rocky planet for the lowest elevation point. Imagine you have a team of human explorers working with you, and they're all exploring around the planet. The team is small, it is quite like they XXX? no explorable/explorator? actually find the lowest elevation point, XXX? for a lot of tall mountains that lead the explorers getting trapped and XXX? the places on the planet. Instead imagine that you have a very large team of explorers and each person XXXly? on the surface of the planet and then start searching for the lowest elevation point. The more explorers you have, the more likely it is that at least one of them will find the lowest elevation point of the planet. At Rosetta@Home, we're instead searching the energy landscape for protein trying to find the lowest energy structure for the aminoacid sequence. The more computers there are doing these searches, the more likely it is that somebody will actually find it. In each step of the Rosetta search process, a move is made in which part of the protein structure is randomly altered. The top left panel of the screensaver shows each move as it is being made. If Rosetta calculates that the energy has decreased with the move, it is accepted, and displayed in the middle panel. The lowest energy structure found so far is displayed in the next panel over. Just below this is the actual shape of the protein, if it is known. The panel to the right tracks how closely each accepted move compares to the known protein structure. The bottom panel tracks the energy of each move. The energy after the most recent move is located on the right. In the bottom right corner is a graph which plot? the energy versus how close the shape is to the actual protein. From this graphic you can tell when you search has entered a new region of the energy landscape. So one of the dreams of many people on this project is that out of the - say million users - on Rosetta@Home, there may be some, maybe some kids, a 9 years old girl in Korea, who grow up looking at this fascinating proteins on the screens and develop a very strong intuitions for what molecules do and are gonna grow up and become great biophisicists and because of this intuition that developed when they were young hopefully they will help solve? the problem immediately. This is a whole new step forward in the relationship between scientists and the public. To solve the problem of protein structure prediction is quite clear that it is really not possible without the contributions of people from all over the world like yourself, because it's such a big computing problem that it just cannot be done with any inhouse resources so we can only do it collaboratively as a collaboration between us and you and through this collaboration we can solve a problem which I really think couldn't be solved otherwise" Thanks in advance, Dario

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