Results 11 to 20 of about 1,274,222 (313)
Mega-scale experimental analysis of protein folding stability in biology and design
Nature, 2023 Large-scale assays using cDNA display proteolysis are used to measure the folding stabilities of protein domains, providing a method to quantify the effects of mutations on protein folding, with applications in protein design.
Kotaro Tsuboyama +8 more
semanticscholar +1 more source
Encyclopedia of Bioinformatics and Computational Biology, 2020 This chapter explores sequence analysis (SA), which conceives the social world as happening in processes, in series of events experienced by social entities. SA refers to a set of tools used to summarize, represent, and compare sequences — i.e.
Andrey D. Prjibelski +2 more
semanticscholar +1 more source
BERTology Meets Biology: Interpreting Attention in Protein Language Models [PDF]
bioRxiv, 2020 Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability.
Jesse Vig +5 more
semanticscholar +1 more source
MOSAL : software tools for multiobjective sequence alignment [PDF]
, 2014 Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of these alignments provide a potential explanation
Monsanto Pinheiro, Miguel +8 more
core +1 more source
Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils.
Journal of Biological Chemistry, 2023 Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This
D. Woolfson
semanticscholar +1 more source
Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition [PDF]
, 2015 This work was supported by a grant from the Biotechnology and Biological Sciences Research Council (REF: BB/M000400/1 to MFW).The adaptive prokaryotic immune system CRISPR-Cas provides RNA-mediated protection from invading genetic elements.
Bolt, Edward +17 more
core +1 more source
Towards an Encyclopaedia of Sequence Biology
, 2018 In this review, I have presented several topics relevant to the present state and to the future state of the scientific field that I propose to call sequence biology (SB). In some pertinent publications, this field was called DNA linguistics.
A. Bolshoy
semanticscholar +1 more source
STAR Protocols, 2023 Summary: This protocol demonstrates how a fragmented reference genome and low-coverage sequencing data can be efficiently utilized for population genetic analyses of a species with highly reduced genetic diversity.
Emmi Olkkonen, Ari Löytynoja
doaj +1 more source
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Molecular biology and evolution, 2013 We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained ...
K. Katoh, D. Standley
semanticscholar +1 more source
Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells
Stem Cell Research, 2014 The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We
Angela Re +4 more
doaj +1 more source