What's the status of using LLMs for vulnerability repair?5 answersLarge Language Models (LLMs) show promise in vulnerability repair but face challenges. Studies on LLMs like Codex and AI21's J-1 demonstrate potential in repairing cybersecurity bugs, with a collective 100% success rate on synthetic scenarios. However, when applied to real-world Java vulnerabilities, LLMs and DL-based APR models fix few issues, with Codex leading but generating many uncompilable patches. Combining LLMs with Formal Verification strategies has shown success rates of up to 80% in repairing C code vulnerabilities like buffer overflows. LLMs have also proven effective in repairing hardware security bugs in Verilog code, outperforming existing tools. Overall, while LLMs hold promise, further innovations are needed to enhance their effectiveness in automated vulnerability repair.
How multisite phosphorylation impacts the conformations of intrinsically disordered proteins?3 answersMultisite phosphorylation impacts the conformations of intrinsically disordered proteins (IDPs) by inducing changes in their structural and dynamical properties. Phosphorylation can expand neutral or overall negatively charged IDPs and shrink positively charged IDPs, leading to changes in their collapse propensity. The distribution of phosphorylated and positively charged residues throughout the sequence plays a crucial role in the impact of phosphorylation on the global dimensions of IDPs. Phosphorylation can also affect the solvation of IDPs, which should be considered when analyzing experimental data. Additionally, multisite phosphorylation can significantly alter the exposure of active sites in IDPs, highlighting their susceptibility to regulation through post-translational modifications. The conformational and structural implications of phosphorylation on IDPs are complex and diverse, and further studies are needed to fully understand the effects of this post-translational modification.
Are drugs selective against a particular intrinsically disordered protein?5 answersDrugs targeting intrinsically disordered proteins (IDPs) have been challenging to develop due to the highly dynamic and heterogeneous nature of IDP structures. However, recent research suggests that drugs can achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. Covalent modification has been proposed as a possible method for targeting IDPs, which could lead to specific and strong binding and inhibitory potential. Additionally, biomolecular condensation, a phase separation process that IDPs undergo, offers opportunities for modulating the activities of IDP targets. While the development of drugs targeting IDPs is still in its earliest stage, initial hits have shown promise in selectively blocking specific interactions of intrinsically disordered transcription factors (TFs) with their protein binding partners. Overall, while challenges remain, there is potential for the development of selective drugs against specific IDPs.
How long polypeptides domains can be inserted in or deleted from a protein structure without disrupting structure?5 answersProtein domains can undergo length variations, such as insertions or deletions, without disrupting the overall protein structure. These length variations can introduce changes at structural, functional, and interaction levels. LenVarDB is a database that traces these length variations across protein domain superfamilies and provides information on the location of these variations within the protein domains. The database allows for the visualization of the length-variant regions on the protein structure and alignment, which can be useful in predicting changes within structurally or functionally relevant sites. Additionally, a study using a Monte Carlo algorithm showed that proteins with one domain inserted into another can be predicted accurately, even with errors in linker conformation. Therefore, it is possible for polypeptide domains to be inserted or deleted from a protein structure without disrupting its overall structure.
What do you mean by disordered phase in crystal?3 answersA disordered phase in a crystal refers to a state where the atoms or particles within the crystal do not exhibit a regular or ordered arrangement. This can occur due to various factors such as temperature, pressure, or defects in the crystal structure. In this phase, the crystal may exhibit properties that are distinct from those of a regular crystal, and may even resemble properties of disordered solids. The transition from a crystal to a disordered phase can be characterized by changes in structural order and density, and can lead to unique behaviors such as particular pressure dependence of elastic moduli and coordination number. The discovery of this transition sheds light on previously unknown aspects of solids.
What is sequence length in llm?5 answersThe sequence length in LLM refers to the length of the generated response by the large language models. LLMs have the ability to accurately perceive and predict the response length with minimal overhead. This information is leveraged to introduce an efficient sequence scheduling technique that groups queries with similar response lengths into micro-batches. By doing so, the inference throughput is improved by 86% without compromising effectiveness. Additionally, it has been observed that the performance of Transformer models, a type of LLM, drops significantly when facing sequences of length diverging from the length distribution in the training data. This suggests that the issue might be in the mismatch between the length distributions of the training and validation data, combined with the tendency of neural networks to overfit to the training data.