相关论文: A New Route for the Determination of Protein Struc…
Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…
Structure determination is a key application of XFELs and 4th generation synchrotron sources, particularly using the coherent and pulsed X-ray radiation from X-ray free-electron lasers (XFEL). Scientific interest focuses on understanding…
The routine atomic-resolution structure determination of single particles is expected to have profound implications for probing the structure-function relationship in systems ranging from energy materials to biological molecules.…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…
A deep understanding of molecular photo-transformations is challenging because of the complex interaction between the configurations of electrons and nuclei. An initial optical excitation dissipates energy into electronic and structural…
X-ray free electron laser (XFEL) experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely…
X-ray free-electron lasers (XFELs) are cutting-edge scientific instruments for a wide range of disciplines. Conventionally, the narrow bandwidth is pursued in an XFEL. However, in recent years, the large-bandwidth XFEL operation schemes are…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields including protein structural modeling. Protein structural modeling, such as predicting…
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…
The three-dimensional structure of proteins plays a crucial role in determining their function. Protein structure prediction methods, like AlphaFold, offer rapid access to a protein structure. However, large protein complexes cannot be…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…