12 papers · ranked by Valyu relevance
Toshitake Asabuki, Claudia Clopath
Recurrent neural circuits often face inherent complexities in learning and generating their desired outputs, especially when they initially exhibit chaotic spontaneous activity. While the celebrated FORCE learning rule can train chaotic recurrent networks to produce coherent patterns by suppressing chaos, it requires…
Morten Nielsen, Claus Lundegaard, Ole Lund
Background Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules.…
Byung-Jun Yoon
Background Sequence alignment has become an indispensable tool in modern molecular biology research, and probabilistic sequence alignment models have been shown to provide an effective framework for building accurate sequence alignment tools. One such example is the pair hidden Markov model (pair-HMM), which has been…
Zhen Tan, Yinghan Fu, Gaurav Sharma, David H. Mathews
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions…
Tao Fang, Damian Szklarczyk, Radja Hachilif, Christian von Mering
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made…
Authors not listed
In molecular machine learning, the choice of the representation of molecules can have a significant impact on model performance. However, understanding the root causes of these performance differences often proves challenging. One promising approach to explore model behavior is representational alignment, which…
Maryam Gillani, Gianluca Pollastri
Alignments in bioinformatics refer to the arrangement of sequences to identify regions of similarity that can indicate functional, structural, or evolutionary relationships. They are crucial for bioinformaticians as they enable accurate predictions and analyses in various applications, including protein subcellular…
Maurits Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra + 3 more
'Wan Fokkink' 'Jaap Heringa' 'Ilya Ioshikhes'] Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still…
Maurits J J Dijkstra, Atze J van der Ploeg, K Anton Feenstra, Wan J Fokkink + 3 more
Multiple sequence alignment (MSA) is one of the fundamental tasks in bioinformatics, essential to a wide variety of workflows, including fold prediction, phylogenetic analysis and mutation impact prediction. The exact solution with dynamic programming is not feasible for more than a handful of sequences. For protein…
Yasmine Nahal, Janosch Menke, Julien Martinelli, Markus Heinonen + 5 more
Machine learning (ML) systems have enabled the modelling of quantitative structure-property relationships (QSPR) and structure-activity relationships (QSAR) using existing experimental data to predict target properties for new molecules. These property predictors hold significant potential in accelerating drug…
Joseph Redshaw, Darren Ting, Alex Brown, Jonathan Hirst + 1 more
Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and timeconsuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating…
Authors not listed
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two important targets in current drug discovery, mainly due to the COVID-19 pandemic and the MERS-CoV outbreaks in recent years. An important target of both SARS-CoV-2 and MERS-CoV is the main…