We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs ...
Multiple sequence alignment (MSA) has long been used as a powerful method to investigate the evolutionary, structural and functional properties of protein families. It is also a fundamental technique in recent deep-learning based protein 3D structure predictors. Though existing MSA methods hav...
Protein ConformationProteinsSequence Alignment算法计算生物学蛋白质构象蛋白质类序列排列Alignment of protein sequences is a key step in most computational methods for prediction of protein function and homology-based modeling of three-dimensional (3D)-structure. We investigated correspondence between gold ...
In contemporary structural bioinformatics, the advent of advanced artificial neural network architectures1,2,3 has ushered in an era where protein structures are predicted with high accuracy for a myriad of protein sequences4,5. This surge in structural data has presented a challenge: the need for...
Thealignmentoftwosequences(DNAorprotein)isarelativelystraightforwardcomputationalproblem.ThebestsolutionseemstobeanapproachcalledDynamicProgramming.DynamicProgramming DynamicProgrammingisageneralprogrammingtechnique.Itisapplicablewhenalargesearchspacecanbestructuredintoasuccessionofstages,suchthat:the...
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules—proteins, RNAs and DNAs. The pipeline is built on a uniform TM-score object...
protein-coding genes can be seen here (A practice using PhyloAln for phylogenomics). For other types of the data, such as non-protein-coding genes or genes with non-standard genetic codes, you can collect the reference sequences fromNCBIor other places, and additionally adjust the options of...
INTRODUCTION IMGT/DomainGapAlign is the IMGT online tool for the analysis of amino acid (AA) sequences and two-dimensional (2D) structures of domains. The use of this tool is described here. Three domain types can be analyzed: the variable (V) and constant (C) domains of the immunoglobuli...
IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell...
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