OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
AlphaFold2 revolutionized structural biology with the ability to predict protein structures with
exceptionally high accuracy. Its implementation, however, lacks the code and data required …
exceptionally high accuracy. Its implementation, however, lacks the code and data required …
Towards the accurate alignment of over a million protein sequences: Current state of the art
Large-scale genomics requires highly scalable and accurate multiple sequence alignment
methods. Results collected over this last decade suggest accuracy loss when scaling up …
methods. Results collected over this last decade suggest accuracy loss when scaling up …
Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology
The recent breakthrough made in the field of three-dimensional (3D) structure prediction by
artificial intelligence softwares, such as initially AlphaFold2 (AF2) and RosettaFold (RF) and …
artificial intelligence softwares, such as initially AlphaFold2 (AF2) and RosettaFold (RF) and …
Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
Sexual reproduction is widespread, but asexual lineages have repeatedly arisen from
sexual ancestors across a wide range of eukaryotic taxa. The molecular changes …
sexual ancestors across a wide range of eukaryotic taxa. The molecular changes …
AQcalc: A web server that identifies weak molecular interactions in protein structures
M Afshinpour, LA Smith, S Chakravarty - Protein Science, 2023 - Wiley Online Library
Weak molecular interactions play an important role in protein structure and function.
Computational tools that identify weak molecular interactions are, therefore, valuable for the …
Computational tools that identify weak molecular interactions are, therefore, valuable for the …
Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues
A Amalfitano, N Stocchi, HM Atencio, F Villarreal… - Genome Biology, 2024 - Springer
Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing
and/or gene model errors and sequences from pseudogenes from complex, eukaryotic …
and/or gene model errors and sequences from pseudogenes from complex, eukaryotic …
Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper
SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of
thousands of protein sequences in time-frames faster than standard structure-based …
thousands of protein sequences in time-frames faster than standard structure-based …
Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
Abstract Sequence alignments are the foundations of life science research, but most
innovation so far focuses on optimal alignments, while information derived from suboptimal …
innovation so far focuses on optimal alignments, while information derived from suboptimal …
Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution
L Yutzy, K Nguyen, P Vallet, J Li, J Yu, R He, L Yan… - 2024 - chemrxiv.org
Directed evolution (DE) mimics natural selection to improve the functions of a target protein.
Machine learning (ML) has significantly streamlined DE by aiding in several steps, which …
Machine learning (ML) has significantly streamlined DE by aiding in several steps, which …
Joint protein sequence-structure co-design via Equivariant diffusion
R Vinod, KK Yang, L Crawford - NeurIPS 2022 Workshop on …, 2022 - openreview.net
Protein macromolecules are known to play key roles in cellular processes. Solving inverse
design problems can allow us to control targeted cellular processes by designing proteins …
design problems can allow us to control targeted cellular processes by designing proteins …