FoldIt Wiki/Учебные головоломки
Здесь вы можете увидеть оригинальные инструкции к решению учебных головоломок.
Боковые цепи (Sidechains)
[править]Уровень 1-1: Одно маленькое столкновение (One Small Clash)
[править]Это белок. Нам нужна ваша помощь, чтобы сложить его в правильную форму!
Предупредите столкновение - кликните на одну из боковых цепей и перетащите в сторону от другой боковой цепи.
Уровень 1-2: Поверните Это (Swing It Around)
[править]Вы не можете видеть боковые цепи с этой стороны!
Кликните на белом фоне и, удерживая нажатой кнопку мыши, двигайте мышью, чтобы повернуть фигуру.
Вы можете переместить фигуру, удерживая клавишу CTRL и сдвигая мышь во время перетаскивания. Вы также можете увеличить или уменьшить фигуру, прокручивая колёсико мыши.
Уровень 1-3: Растрясите Это наружу (Shake It Off)
[править]Основание белка красное с столкновениями! Сделайте основание белка зелёным.
Инструмент Shake Sidechains помогает найти лучшие места для всех боковых цепей сразу. Используйте этот инструмент!
Упаковка основания белка
[править]Уровень 2-1: Когда основания сталкиваются (When Backbones Collide)
[править]Это столкновение не может быть исправлено только лишь перемещениями боковых цепей!
Кликните и перетащите большое основание белка, чтобы развернуть его.
Уровень 2-2: Заполнить зазор (Close the Gap)
[править]Этот белок должен быть сложен вместе!
Приблизите две половины так близко, чтобы гидрофобные боковые цепи соответствовали друг другу. Потом попробуйте инструмент Wiggle Backbone, чтобы основание медленно приобрело лучшую форму.
Level 2-3: Wiggle
[править]You now have access to a VERY powerful tool: the WIGGLE tool! Just like SHAKE tries to take care of sidechains, WIGGLE tries to let Foldit improve the backbone. WIGGLE gets stuck if it cannot increase the score. Click this button again to stop the tool.
Уровень ?: Двойная упаковка (Twin Pack)
[править]Фигурные винты слишком далеко друг от друга!
Упакуйте спирали тесно, так чтобы гидрофобные боковые цепи оказались сплющенным между ними. Потом используйте инструменты Shake и Wiggle.
Даже если ваша оценка снизилась, попробуйте сочетание Shake и Wiggle, чтобы получить больше баллов!
Уровень ?: Тройная упаковка (Triple Packed)
[править]Гидрофобные боковые цепи в центре открыты!
Вы можете "заморозить" (инструмент Freeze) части белка, чтобы удержать их на месте во время спуска. Просто удерживайте shift и дважды щелкните область, которую вы хотите закрепить.
Так как у многих возникают проблемы с этой головоломкой, то приходится начинать решение несколько раз: Если вы сделали много ошибок, то перезагрузите головоломку (лучше делать это из меню, если вы повернули фигуру).
Теперь, когда головоломка обновлена, сделайте следующее: Возьмите за верхнюю спираль в точке, где указывает стрелка подсказки. Теперь переместите мышь вниз, в направлении красных шаров.
Если начинаются столкновения боковых цепей, то потяните немного больше, и остановите. Теперь Shake и Wiggle.
Водородная связь
[править]Уровень 3-1: Листы вместе (Sheets Together)
[править]Этот белок состоит из двух плоских листов.
Стяните эти листы вместе! Они любят это.
Уровень 3-2: Одинокие листы (Lonely Sheets)
[править]Два маленьких листа, потерянные и одинокие ...
Помогите им найти друг друга с Rubber Band: удерживайте нажатой клавишу shift, щелкните на одном листе и перетащите его к другому листу. Нажмите Wiggle чтобы начать их перемещения.
Уровень 3-3: Листы и Лестницы (Sheets and Ladders)
[править]Три листа были оторваны друг от друга!
Соедините их вместе, кликая на них и перетаскивая, удерживая нажатой клавишу Shift. Как только они будут достаточно близко, Вы можете отпустить клавишу Shift и нажать Wiggle.
Уровень 3-4: Заблокируй и Отпусти (Lock and Lower)
[править]Один из листов не на месте!
Резиновые полосы могут удерживать листы соединёнными. Запомните, что вы также можете "заморозить" их нажатием кнопки Shift и щелчком мыши, и включить Shake и Wiggle, как только они окажутся достаточно близко друг к другу.
Уровень 3-5: Перестрой (Rebuild)
[править]You might have guessed by now, but color is used to show how well part of the protein is folded.
This loop appears to be a problem. You can deal with problematic segments by using the REBUILD tool. Rebuild tests out different shapes for the protein. Right click (for windows) on the backbone to start a Rebuild. You can stop when Rebuild finds the shape you want. Shake and Wiggle will take care of clashes. This looks like a good shape! Try a Shake and Wiggle to clean it up. You can Wiggle a single section. Right click and choose Wiggle
Madde's video: http://www.youtube.com/watch?v=V-AiFAO_xgo
Гидрофобность и гидрофильность
[править]Уровень 4-1: Скройте гидрофобную цепь (Hide the Hydrophobic)
[править]Большая гидрофобная боковая цепь выходит в открытое пространство!
Оранжевая боковая цепь должна находиться внутри белка. Уберите её в пустое пространство во внутренней стороне белка и разверните синие гидрофильные боковые цепи наружу.
Уровень 4-2: Переверни это (Turn It Down)
[править]Спираль была повёрнута и гидрофобные боковые цепи оказались снаружи!
Поверни её обратно на место инструментом Tweak(Настройка).
Вы начали настройку!
Нажмите на сиреневую стрелку и удерживайте кнопку мыши нажатой чтобы вращать белок в нужном вам направлении.
Следите за счётом! Если вы повернёте белок слишком далеко, то вы можете повернуть его обратно или просто Отменить действие (Undo).
Level 4-3: Flippin' Sheets
[править]One of the sheets is twisted the wrong way!
Look for the sheet with the exposed hydrophobics, and click the new straight arrows on the Tweak tool to shift and flip it.
You've started a Tweak!
Click and hold on the curved purple arrows to rotate the protein in the direction you want it to go or use the straight purple arrows to shift and flip the sheet in that direction.
Watch your score! If you turn it too far, you can try turning it back or just Undo.
LennStar's guide: This is one puzzle that really dislikes being mishandled. It took me at least 5 tries. This is how to do it: If you already have done anything to it, reset the puzzle. (Hint: You propably have to move the 4 sheets to the foreground, the one with the arrow pointing on with the short end to the left. You can also go back to puzzle menu to get the right view.)
Now right click on the one sheet where the arrow from the text points to. Click tweak. Now click one time on the straight arrow to the right. Now the sheet should flip. use shake and wiggle it. That should raise your score to the needed points.
Level 4-4: Правильный поворот (The Right Rotation)
[править]Найди ту спираль, которую нужно повернуть, и исправь это инструментом Tweak!
Поищи гидрофобные цепи, повёрнутые наружу, и поверни их внутрь. Ты всегда можешь нажать Отменить.
Level 4-5: Changing the structure
Changing the structure of the protein can help you see a solution better, and also affects Rebuild and Tweak. These three segments should be sheets. To enter Structure mode, click the Modes tab and choose Structure, or press 2. Right click a section of the protein while in structure mode to asign its structure from the three secondary structure types. Once you've done that, try using tweak to flip the sheet down. Use Shake and Wiggle to finish up. If the protein starts coming apart, you can use reset or undo.
Tip : click on pull mode, flip the sheet with the left arrow or rebuild the last part of the sheet.
Madde's video : http://www.youtube.com/watch?v=TfXeSc4AyA8
Tools and Types
[править]Уровень 5-1: Quest to the native (QTTN)
[править]In this puzzle, the correct solution, called a NATIVE, is known. To align the guide with a specific section of the protein, Right click any segment and click ALIGN GUIDE. Use the tools available to match the protein with the guide. If you haven't discovered it yet, you can attach a rubber band from the protein to a point in empty space. Rubber bands also affect the pull tool, not just wiggle. Remember to freeze parts of the protein that you don't want warped by wiggle or pull.
Уровень 5-2: Movin' along
[править]Sometimes you can MOVE whole pieces of the protein. Click on a piece to bring up the MOVE tool. Then press and hold down RIGHT BUTTON anywhere on the tool to drag the piece around. You can't pull on the backbone of this puzzle.
Tip : Click on the helix, then on the purple star with the right button, then move the helix on the shadow, rotate the view to check then shake and wiggle. Dont use Align tools, if you have use it, go to intro puzzle menu then to movin along to refresh the view.
Madde's video : http://www.youtube.com/watch?v=Q2x03y6e4Kk
Уровень 5-3: Electron density
[править]In an Electron Density puzzle, we only have data on the rough shape of the protein. You are given this data as a 3D surface that predicts the general areas where parts of the protein are located. The backbone of the protein will fit neatly inside the 3D region, but it's up to you to work out how it fits. Click on the ELECTRON DENSITY button. These options let you control how the density surface is drawn. Adjust the THRESHOLD to change the thickness of the density region. At a good threshold, you can see shapes in the region that match parts of the protein. After moving the protein press ALIGN PROTEIN TO DENSITY to line up the surface with the protein. The alignment usually takes a few seconds to complete. Use Shake, Wiggle, and careful moving to fold the protein into the best possible shape that fits inside the predicted region.
Tip : wiggle, shake, wiggle, shake, then drag the end of protein inside the cloud with caution, skahe, wiggle. vidoe : http://www.youtube.com/watch?v=jDOY1QIGkog
Уровень 5-4: Exploration
[править]In exploration puzzles like this one, your goal is to find a solution that is different from the starting structure. Your calculated score will be the protein's base score times an exploration multiplier for finding new configurations. You can use the Contact Map to help you find new configurations for the protein. The rows and columns in Contact Map correspond to segments of the backbone. A black mark indicates that the segments corresponding to that row and column are in contact. The red areas are contacts present in the starting structure. White areas are new contacts, which increase your score multiplier. You can click on TUTORIAL to learn more about Exploration puzzles. Use all the tools you have learned to fold this protein into a new shape. Don't be afraid to break some connections to make new ones. Try lining up all 4 sheets.
Madde's video :http://www.youtube.com/watch?v=AAh3ThsxohQ
Уровень 5-5: Контроль над столкновением (Control over clashing)
[править]You may have noticed that using Wiggle when there are many clashes causes the protein to come apart. To avoid this, lower the CLASHING IMPORTANCE . This lets Wiggle keep making small adjustments even if the protein is packed too tight. A lower Clashing Importance also lets you make moves that add clashes without unravelling the protein, like pulling on a tangled strand. Try setting Clashing Importance to 0.1, then Wiggle while slowly increasing it.
Madde's video: http://www.youtube.com/watch?v=TdC-9fmXdjY
Sequences
[править]Level 6-1: Basic Threading
These levels will introduce the powerful ALIGNMENT tool! It will let you use the structures of real proteins, called TEMPLATES, by THREADING. Click on the smiley button to bring up the ALIGNMENT tool. This 3D strcutures shows the backbone of the template. The bottom row of the letters is the TEMPLATE SEQUENCE. you can see it in 3D as spheres connected by lines. The top row of letters is the sequance of your protein. The cylinders in 3D show how its backbones lines up with the template.
When you THREAD, your protein will try to fit onto the 3D template where the cylinders are. Click the little smiley to try threading. Now that you've threaded it, try a shake and wiggle!
In this puzzle, you'll just need to use the ALIGNMENT tool to thread, then wiggle and shake. Don't worry about making manual adjustments. In this puzzle, you'll just need to use the ALIGNMENT tool to thread, then shake and wiggle.
Level 6-2: Alignin' Sequences
Bring up the alignment tool again. This time the letters and colors in the sequences are not lined up well.This middle row shows how well each letter matches; a bigger white bar means a better match. And this score (on the right) shows how the sequences match overall . You can click and drag or use the arrow keys to move the letters around. You can reset, undo, or redo with these buttons (on the left). Try to line up the colors. It's okay if there are spaces, but fewer spaces is better. Click here to thread when they match well! (the little smiley).
Threading didn't work. Try to find a better match. Letters that blink red after trying to thread are causing problems.
With a good alignment, you'll just need to use the ALIGNMENT tool to thread then wiggle and shake.
Don't worry about making manual adjustments. With a good alignment, you'll just need to thread, shake, and wiggle.
Level 6-3: A major shift
The sequences don't always line up perfectly. You can look at the template structure to get an idea of what threading will do. A space in your sequence will stretch your protein when it is threaded. A space in the template sequence will squash your protein when it is threaded. Use the sequences to line this purple part up and make a good sheet; watch how the 3D structure moves when you change the aligment. But be careful how you align this loop! Look at the structure and keep any stretched segments away from the rest of the protein.
If shake and wiggle doesn't work, try a different alignment!
Threading didn't work. Put the only space after this letter! Letters that blink red after trying to thread are causing problems. Put the only space after this letter! (The first G)
Tip : see the image, wait for the thread a long time, shake a long time and wiggle.
Protein Design
[править]Level 7-1: Intro to Design
Welcome to the design puzzles. In these challenges you will have the power to design new proteins! Segments with brighter colors can be designed! Some of these sidechains are too large. You can change them in Design Mode. To enter Design Mode, click the Modes tab and choose Design, or press 4. Select the segments you want to mutate. Click the Mutate Button from the menu. Then click the picture of the sidechain you want to mutate to Try to find better fits for both designable sidechains. If you're stuck, it may be easier to restart from the beginning.
Level 7-2: Swapping Side Chains
Now some sidechains are too small, causing voids! Try replacing them with some large ringed hydrophobics.
You'll need to change to Design Mode.
Level 7-3: Mass Mutate
This helix has lot of unburied orange hydrophobics.You can change them to blue hydrophilics in Design Mode. You've earned a new tool! Mutate Sidechains is like Shake, but may mutate designable sidechains. Stop the Mutate Sidechains by pressing the space bar.
Dont reset on this puzzle, go to menu/ intro puzzle and click on mass mutate.
Level 7-4: Insertion and Deletion
This red line is a CONSTRAINT, indicating that the segments it connects should be closer together. You can change the length of the helix by inserting or deleting segments. Right click a segment of the helix and use Insert Between. The blue blinking segments will show you where it will appear. The protein seems a little short now. You may want to undo or insert a segment. You can use wiggle and mutate sidechains to finish up. The protein seems a little long now. You may want to undo or delete a segment.
More molecules
[править]Level 8-1: Ligand debut
These levels contain molecules other than proteins! This small molecule is a LIGAND. Proteins can be designed to bind ligands. Hydrogen bonds are important for binding ligands. Connect red atoms with blue atoms to form bonds between the ligand and sidechains! Left click on the ligand to bring up MOVE tool. RIGHT-button-drag to move left, right, up, and down, LEFT-button-drag to rotate and SHIFT-LEFT (or MIDDLE) -button-drag to move ligand Into/Out of screen. When the ligand is in a good place, try a wiggle!
Level 8-2: Ligand constraints
These are CONSTRAINTS. Red constraints are violated. Make the constraints become green! After moving the ligand closer, use WIGGLE SIDECHAINS to wiggle the sidechains and the ligand at the same time. Try and compare it to Shake Sidechains.
Level 8-3: DNA Pairing
Use Design Mode to find the correct match for the incorrectly paired sidechains. DNA sidechains pair according to color and size. Match sidechains of same color and opposite sizes to make lots of bonds!
Match sidechains of the same color and opposite sizes to form lots of hydrogen bonds! Look at this big yellow sidechain with a small yellow sidechain. Use Design Mode to find the right match for the incorrectly paired purple sidechains!
Level 8-4: DNA and Protein
DNA can hydrogen bond to protein. Mutate the proteins to form better bonds. Try adding a long hydrophilic here. Try a shorter, forked hydrophilic here