Scoring residue conservation

By William S. J. Valdar. Proteins: Structure, Function, and Bioinformatics, 2002

665 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/900f2340c6354edcc64e4272d36e04a5901541e0

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Janet M. Thornton
2. Roman A. Laskowski
3. John A. Capra
4. Mona Singh
5. Christine A. Orengo
6. Nir Ben-Tal
7. C. Bailey‐Kellogg
8. Naren Ramakrishnan

In Molecular Biology

1. Tal Pupko
2. Nir Ben-Tal
3. C. Bailey‐Kellogg
4. Janet M. Thornton
5. John A. Capra
6. Mona Singh
7. Roman A. Laskowski
8. Itay Mayrose

In Spectroscopy

1. Roman A. Laskowski
2. John A. Capra
3. Mona Singh
4. Nir Ben-Tal
5. C. Bailey‐Kellogg
6. Janet M. Thornton
7. Naren Ramakrishnan
8. Christine A. Orengo

Citations in the corpus

• Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure (2009, background): “fewer mutations relative to the rest of the protein [22].”
• Predicting protein function from sequence and structure (2007, methodology): “Other methods for identifying FDRs in protein families exploit entropy-based approache”
• Graphical models of residue coupling in protein families (2005, background): “Since there are multiple, overlapping, taxonomies of amino acids [27] we can even assume a hidden variable model (de-noting an unknown relabeling of each residue) and attempt to infer the network as well as the relabeling function from a given MSA and contact map.”
• Graphical Models of Residue Coupling in Protein Families (2008, background): “For example, amino acid conservation has long been recognized as an important indicator of structural or functional significance [ 25 ].”
• Improved prediction of protein-protein binding sites using a support vector machines approach. (2005, methodology): “…sequences (E-values below 10−4 and limited to at most 100 sequences) from the BLAST search, together with the query sequence were aligned with CLUSTALW (Thompson et al., 1994), and a conservation score at each residue position was then calculated using the Scorecons program (Valdar, 2002).”
• A family of evolution-entropy hybrid methods for ranking protein residues by importance. (2004, background): “In one of the earliest attempts to quantify the conservation of a residue at certain alignment pos- ition, Zvelebil et al. converted the count of residues with a certain property (hydrophobicity, size, etc.) into a property called conservation number, which enabled them to distinguish poorly conserv”
• Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, neutral): “M is defined by Valdar et al. 50 as follows: where m is a modified PET substitution matrix.”
• A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation (2009, methodology): “The alignment was scored at the missense position for conservation using Scor-econs 41 , with scoring method ‘valdar01’, matrix ‘modified PET91’, and matrix transformation ‘karkinlike’.”