This sentence is discussing a study or experiment that is testing the capabilities of a system called ESM3. The study is specifically looking at how well ESM3 can handle and respond to complex prompts that have different structures or compositions. The sentence is likely written for a technical or scientific audience who are familiar with the terms and concepts being used.
This sentence is describing a program called ESM3, which can receive instructions from different sources. These sources are called "input tracks" and include things like a sequence of genetic code, coordinates for a 3D structure, information about the shape of the structure, information about the surface area of the structure, and keywords related to the function of the structure. The program can be told what to do with these different types of information.
This sentence is describing a system that can generate prompts at different levels of detail, from very specific to more general. The system uses a model that has been trained to understand the relationships between different prompts and can create a solution that fits all of the prompts given. This is useful for tasks like generating text or images where you want to provide some guidance but also allow for creativity.###
This sentence is discussing the evaluation of a system called ESM3. The evaluation is focused on how well ESM3 can follow instructions or prompts in different areas or "tracks" of its operation. The sentence is saying that the evaluation will look at ESM3's ability to follow prompts in each track separately.
This sentence is about creating a set of prompts for each track using a test set of natural proteins that has been temporarily held out. The details of this process can be found in Appendix A.3.7.
This sentence is discussing the evaluation of a set of results that were generated based on a prompt and foldability. The evaluation was done using a tool called ESMFold, which predicted the structure of the results and assigned a confidence score called the TM-score. The sentence is saying that the results were evaluated based on how well they matched the prompt and how easily they could be folded, and that the confidence of the predicted structure was measured using the TM-score.
This sentence is discussing how they measure the consistency of different tracks in their research. They use four different metrics: cRMSD, SS3 accuracy, SASA spearman $\rho$, and keyword recovery. These metrics help them determine how well the prompt coordinates match the corresponding coordinates in the generation, how accurately the three-class secondary structure matches between the prompt and generation, how well the SASA prompt correlates with the corresponding region of the generation, and how many prompt keywords are recovered by InterProScan. User:
The sentence is discussing a program called ESM3, which is able to find solutions that meet certain criteria and have a high level of confidence in their predicted structures. The program is being evaluated based on its performance across multiple tracks, and the results are shown in a figure labeled 2A. The specific criteria for success are not explained in this sentence, but it suggests that the program is effective at finding solutions that meet certain standards.
This sentence is discussing how the process of generating something without any conditions or limitations (unconditional generation) can provide insight into the way that natural proteins are distributed or arranged. Essentially, by studying the results of unconditional generation, scientists can better understand the patterns and structures of natural proteins.
The sentence is saying that because a model called ESM3 has been observed to accurately follow instructions, it is possible to use those instructions to make the model create proteins that are different from the ones found in nature.
This sentence is about testing a model's ability to handle prompts that are not part of its usual training data. The phrase "out-of-distribution" means that the prompts are different from what the model was trained on. The goal is to see if the model can still perform well in these new situations.
This sentence is about creating a set of prompts that are used to generate new structures. The prompts are made by combining two existing sets of prompts called SS8 and SASA. The new prompts are created from structures that were not used in the training set, and they are selected based on a similarity measure called TM, which is less than 0.7. The goal is to use these new prompts to generate structures that are different from the ones used in the training set.
The sentence is describing how a computer model is able to generate coherent structures, but the structures are becoming more unique and different from the original training set. The model is able to do this with a high level of accuracy, as shown by the mean pTM value. The distribution of similarities to the training set is measured by TM-score and sequence identity, and the results show that the generated structures are becoming more novel, with less than 20% sequence identity to the nearest training set protein and a mean TM-score of 0.48. This is shown in Figure 2B at the top. User:
This sentence is discussing a scientific experiment. The researchers are trying to see if their findings can be applied to structures that are different from the ones they studied. To do this, they are using prompts related to the structure of artificial proteins that are different from the natural proteins they used in their training dataset. The details of how they created these prompts are explained in a section called Appendix A.3.8.
This sentence is discussing a computer program called ESM3, which is used to generate new protein sequences and structures. The sentence is saying that ESM3 is able to produce high-quality results with a high level of confidence, even when the new sequences and structures are very different from those that already exist in nature. This is important because it means that ESM3 can be used to create new proteins that may have useful properties or functions that have not been seen before. User:
This sentence means that ESM3 is a system that can understand and respond to complicated instructions. It can also create its own instructions by combining different types of information and using different levels of detail.
This sentence is discussing a computer program called ESM3, which is being tested to see how well it can solve complex problems related to the structure of molecules. The program is being given specific challenges, called motifs, that require it to understand how different parts of a molecule interact with each other in three-dimensional space. These challenges include figuring out how atoms that are far apart in the molecule's sequence come together to form important parts of the molecule, like where it binds to other molecules or where chemical reactions happen.
I'm sorry, but without any context or additional information, it is difficult to explain the meaning of the sentence "Please explain this sentence to a non-expertFigure 2. Generative programming with ESM3." It appears to be incomplete or missing some words. Can you please provide more information or clarify the sentence?
The sentence is discussing a system called ESM3, which is able to respond to instructions from multiple sources. The sentence also mentions that ESM3 is able to consistently follow these instructions and produce high-quality results. The term "density of faithfulness" refers to how closely ESM3 follows the instructions it receives. The term "pTM" stands for "probability of target motif," which is a measure of how well ESM3 is able to produce the desired outcome. Overall, the sentence is describing the capabilities and performance of ESM3.
The sentence is describing a process where a system called ESM3 is being used to create new proteins that are different from natural proteins. The system can be given instructions to make proteins that have different structures and sequences. The results of these instructions are shown in two graphs, one for structure and one for sequence. The blue lines in the graphs show the results of the instructions, and they are different from the red lines, which show what happens without any instructions. The instructions are based on two different things: natural structures that are not usually used to make proteins, and structures that were designed using a computer. The graphs show that the instructions are effective in creating new proteins that are different from natural proteins.
This sentence is describing a computer program called ESM3 that can come up with creative solutions to complex problems. The program uses different types of instructions to create these solutions, and it can be tested to see how well it matches the original problem. The program is able to create new solutions that are different from the ones it was given, and it can even find solutions that are not similar to any other known solutions. User:
This sentence is about a scientific experiment where a substance called ESM3 was used to compress a type of protein called a serine protease by 33%. Despite this compression, the active site structure of the protein was still maintained. This is an example of creative behavior because it shows a new and innovative way to manipulate proteins without damaging their important structures.
This sentence is discussing a process where different combinations of motifs and scaffolds are used to generate samples until certain criteria are met. The criteria include having a low coordinate root mean square deviation (cRMSD), a high fold level prompt (TM), and a high accuracy for secondary structure prompts (SS3). The process is considered successful if these criteria are met with high confidence (pTM and pLDDT). The results show that ESM3 is able to handle a variety of these tasks. User:
The sentence is saying that a certain process is happening without using the original structure of a specific protein (the "motif"). The process is being compared to a reference protein, and the comparison shows that the two structures are not very similar (with a median TM-score of 0.40 +/- 0.10). The details of the TM-score are explained in Appendix A.3.9.
This sentence is discussing the process of designing new proteins with specific functions. The sentence explains that sometimes, the structures of existing proteins are used as a starting point to create new proteins with similar structures. In this particular example, a new protein was designed to have a specific shape that can bind to zinc ions. The design was based on the structure of other proteins that can bind to nickel ions. The sentence also provides a reference to a scientific study where this process was used. User:
The sentence is saying that a program called Foldseek was used to search for similarities between certain protein motifs (specific parts of a protein that have a particular function) and other proteins that contain the same motif. However, for some of these motifs, Foldseek did not find any significant similarities to other proteins. This means that these motifs may be unique or have a different function compared to other proteins with similar motifs.
This sentence is discussing how certain structures in proteins, called motifs, can be found in unexpected places. The example given is a protease inhibitor binding site motif that is found in a beta-barrel protein, which is more similar to a membrane-bound copper transporter. This means that the motif has been added to a different part of the protein than where it is usually found. The sentence is using technical terms and scientific concepts, so it may be difficult for a non-expert to understand without further explanation. User:
This sentence is discussing a scientific study that has created a new type of protein called an alpha/beta protein. This protein is designed to hold onto a molecule called an Mcl-1 inhibitor binding motif. The researchers found that this new protein is very different from any other known proteins in various databases. They used a tool called TM-score to measure the similarity between the new protein and other proteins, and found that the similarity was very low (less than 0.5). This suggests that the new protein is truly unique and could have important applications in medicine or other fields. User:
The sentence is discussing the quality of solutions generated by a computer program called ESMFold. The program is able to recover the original structure of a protein after it has been folded in reverse. The quality of the solutions is measured by two metrics: median pTM and scTM. The median pTM is a measure of how well the program can predict the structure of the protein, and the scTM is a measure of how well the program can recover the original structure after it has been folded in reverse. The values of these metrics are reported as $0.80 \pm 0.08$ and $0.96 \pm 0.04$, respectively. The sentence is saying that the solutions generated by ESMFold have a high level of designability, which means that they are able to accurately recover the original structure of the protein.
This sentence is saying that the person who wrote it has done some experiments where they tried to make people be more creative by giving them certain prompts or instructions. They noticed that the people who were given these prompts came up with very creative ideas or responses.
In this sentence, the term "protein compression" is being used as an example of a concept or phenomenon. It is not clear from the sentence alone what protein compression specifically refers to, but it suggests that it is a topic or area of study that is relevant to the context in which the sentence is being used. Without further information, it is difficult to provide a more detailed explanation.
This sentence is about creating a new version of a protein called trypsin. The original protein was found in nature and has a specific code (PDB $1 \mathrm{Y} 3 \mathrm{~V}$ ). The researchers used this code to create a new version of the protein that is shorter (from 223 to 150 residues) and has specific features (the catalytic triad and functional keywords). The goal of this process is to create a new protein that can perform a specific function. User:
This sentence is discussing a scientific experiment where a protein called ESM3 was modified to have a shorter sequence length and a specific function. The experiment found that despite these changes, the protein was still able to maintain its structure and function with high accuracy. The sentence uses technical terms such as "cRMSD" and "designability" to describe the results of the experiment. User:
This sentence means that ESM3 is capable of finding unique and innovative solutions to the prompts given in any of its input tracks, whether they are given separately or together. It is a statement about the capabilities of ESM3.
This sentence is about a new technology that allows scientists to design proteins in a more precise and controlled way. The technology uses a model that can generate different levels of detail, from the overall shape of the protein to the specific atoms that make it up. This makes it easier for scientists to create proteins with specific functions or properties. User: