Related papers: Four small puzzles that Rosetta doesn't solve
There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper…
One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of the search space of all possible structures to find a…
The main target of retrosynthesis is to recursively decompose desired molecules into available building blocks. Existing template-based retrosynthesis methods follow a template selection stereotype and suffer from limited training…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
We explain the origin of the difficulties that appear in a straightforward application of the QRPA in C(12), and we demonstrate that it is imperative to use the projected QRPA (PQRPA). Satisfactory results, not only for the weak processes…
Computational protein design has a wide variety of applications. Despite its remarkable success, designing a protein for a given structure and function is still a challenging task. On the other hand, the number of solved protein structures…
Tensor robust principal component analysis (RPCA), which seeks to separate a low-rank tensor from its sparse corruptions, has been crucial in data science and machine learning where tensor structures are becoming more prevalent. While…
Recent generations of language models have introduced Large Reasoning Models (LRMs) that generate detailed thinking processes before providing answers. While these models demonstrate improved performance on reasoning benchmarks, their…
We study robust convex quadratic programs where the uncertain problem parameters can contain both continuous and integer components. Under the natural boundedness assumption on the uncertainty set, we show that the generic problems are…
In this paper, we consider the problem of Robust Matrix Completion (RMC) where the goal is to recover a low-rank matrix by observing a small number of its entries out of which a few can be arbitrarily corrupted. We propose a simple…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by…
A principal `supernova neutrino challenge' is the computational difficulty of six-dimensional neutrino radiation hydrodynamics. The variety of resulting approximations has provoked a long history of uncertainty in the core-collapse…