We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by ...
The inclusion of IM data helped improve structure prediction for all 25 proteins in the experimental dataset. However, there were 8 cases where the RMSD of the selected model (even after improvement) was greater than 5.5 Å (five of those eight cases had TM-Scores less than 0.5). This...
The study of protein structure is an intensely active area of research. The number of proteins for which a three-dimensional structure has been solved has increased exponentially in recent years, and there are currently over 56,000 entries in the Protein Data Bank (PDB [1,2]), a publicly a...
The second approach to model the unknown structure associated with a protein sequence is the “template-free modeling approach”. Most of the programs that deal with this approach assemble, with different strategies, fragments of known proteins and perform refinement of the assembled model in an ite...
4.3. The use of free electron lasers (FEL) Although the use of conventional synchrotron radiation has revolutionized the field of membrane protein structure determination, the growth of well-diffracting crystals of sufficient size for X-ray studies is still a challenge. In addition, as described ab...
when the protein components in two entries had more than 30% identity, we kept the one having better resolution and more structural completeness for further analysis. We have also visually checked each structure with molecular visualization software, and when there were two identical molecules in one...
software. PSIPRED is supplied in source code form - it must be compiled before it can be used. The code should compile on any ANSI C compiler e.g. the GNU C compiler. Please see the LICENSE file for the license terms for the software. Basically it's free to anyone (including ...
Standard proteomic analysis of the tryptic and multi-protease datasets was performed using the free and open-source search software program MetaMorpheus [71]. A custom branch and docker image of MetaMorpheus was created (GitHub: https://github.com/smith-chem-wisc/MetaMorpheus/tree/LongReadProteoge...
(i.e. building blocks can collide and cross-link only via rotation about their centre of mass). To investigate the structural changes due to the restriction of free rotation of high AR building blocks when AR > ARc, we use SANS to probe the network structure of pL hydrogels (Fig.2...
structure of GO annotations. More attractive strength of FAG-EC and HC-Wpin is their efficiencies. The total time complexities of FAG-EC and HC-Wpin are both O(k2m). As is well known the scale-free of protein interaction networks,kis very small and can be considered as a constant. ...