AL2CO: calculation of positional conservation in a protein sequence alignment

By Jimin Pei, Nick V. Grishin. 2001

508 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, background): “Structural elements (arrow for strand and cylinder for helix) and conservations (calculated by Al2Co [59]) are indicated above/below the corresponding sequences.”
Large-scale determination of previously unsolved protein structures using evolutionary information (2015, background): “These insights derive in part from the distribution of evolutionarily conserved residues in the models, as conserved sequence motifs tend to mark functional sites in structures ( Zuckerkandl and Pauling, 1965 ; Villar and Kauvar, 1994 ; Pei and Grishin, 2001 ; Muth et al., 2012 ).”
Tools for integrated sequence-structure analysis with UCSF Chimera (2006, methodology): “Sophisticated methods for calculating conservation are provided by the AL2CO program of Pei and Grishin [8]: entropy-based, variance-based, or sum of pairs, with or without sequence weighting.”
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation (2013, background): “…the number of aligned sequences observed in the mutated position in the whole alignment and the conservation index of the mutated position [35]); iv) 4 elements features from the output of PANTHER algorithm [26] encoding for the probability of deleterious variations, the frequencies of…”
The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics (2013, methodology): “Finally, the multiple sequence alignment was input to the program AL2CO [58] to calculate the conservation score for human and primate proteins.”
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies (2004, methodology): “The AL2CO algorithm [ 46 ] (window size 3) is used to calculate the entropy-based conservation index for each position in the query profile and in the library domain profile.”
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type (2019, methodology): “Sequence conservation scores of the multiple sequence alignment of orthologs were calculated by AL2CO [93] and used as one feature.”
Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation (2015, background): “Conservation index score: 9 is the highest, ≥5 is significant (46).”
SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks (2013, unknown): “We computed conservation indices for each modified lysine by: (1) counting the number of conserved lysines across the seven queried species and (2) using AL2CO on the alignment (Pei and Grishin, 2001).”
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants (2011, background): “We derive for each mutation: the frequency of the wild type, the frequency of the mutated residue, the number of totally and locally aligned sequences and a Conservation Index (CI) [48] for the position at hand: the more a residue is functionally important the more is conserved over evolution.”
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, unknown): “Most of the sequence-based approaches (Capra and Singh, 2007; Pei and Grishin, 2001; Valdar, 2002; Wang et al., 2008) are based on the presumption that functionally important residues are preferentially conserved during the evolution, because natural selection acts on function.”