Protein contact map prediction is a critical and vital step in protein structure prediction, and its accuracy is highly contingent upon the feature representations of protein sequence information and the efficacy of deep learning models. In this pape...
AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates, and disease-causing point mutations often ca...
Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec...
We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure pred...
Molecular phylogenetics and evolution
Aug 16, 2023
Selecting the best model of sequence evolution for a multiple-sequence-alignment (MSA) constitutes the first step of phylogenetic tree reconstruction. Common approaches for inferring nucleotide models typically apply maximum likelihood (ML) methods, ...
The discovery of selective and potent kinase inhibitors is crucial for the treatment of various diseases, but the process is challenging due to the high structural similarity among kinases. Efficient kinome-wide bioactivity profiling is essential for...
Current opinion in structural biology
Jun 13, 2023
Recent breakthroughs in protein structure prediction have increasingly relied on the use of deep neural networks. These recent methods are notable in that they produce 3-D atomic coordinates as a direct output of the networks, a feature which present...
Sequence alignment is an essential component of bioinformatics, for identifying regions of similarity that may indicate functional, structural, or evolutionary relationships between the sequences. Genome-based diagnostics relying on DNA sequencing ha...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2023
The encounter of large amounts of biological sequence data generated during the last decades and the algorithmic and hardware improvements have offered the possibility to apply machine learning techniques in bioinformatics. While the machine learning...
AlphaFold2 and related computational systems predict protein structure using deep learning and co-evolutionary relationships encoded in multiple sequence alignments (MSAs). Despite high prediction accuracy achieved by these systems, challenges remain...
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