Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

By Fabrice Armougom, S. Moretti, O. Poirot, S. Audic, Pierre-Jean Dumas, B. Schaeli, Vladimir Keduas, Cédric Notredame. Nucleic Acids Res., 2006

540 citations recorded by the source corpus.

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on .

Subfields: Information Systems and Management, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/172604b18bc2b22e4219a6e9b47a48c51ffde7d5

How researchers see this paper

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

In Information Systems and Management

1. Daron M. Standley
2. Kazutaka Katoh

In Molecular Biology

1. Kazutaka Katoh
2. Erik S. Wright
3. Daron M. Standley
4. Nick V. Grishin
5. Tal Pupko
6. Jimin Pei
7. Haim Ashkenazy
8. Eric Martz

In Pharmacology

1. Erik S. Wright

Citations in the corpus

• MAFFT-DASH: integrated protein sequence and structural alignment (2019, methodology): “MSA software such as Expresso (8,9) in the TCoffee package and PROMALS3D (10) allow structural information to be incorporated in order to improve accuracy when aligning remote sequence homologs.”
• ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids (2010, methodology): “The user can choose to align the sequences using one of the following leading alignment algorithms: MAFFT (32), T-COFFEE (EXPRESSO mode) (33), PRANK (34) MUSCLE (35) and CLUSTALW (36).”
• Cysteine cathepsins: From structure, function and regulation to new frontiers (2011, methodology): “ture of human cathepsin L (1icf) [74] using the Expresso (3D-Coffee) program [364].”
• T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension (2011, methodology): “The most recent improvement in T-Coffee has been the development of the concept of template-based multiple sequence alignment (16,17).”
• DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment (2015, background): “Those programs that have integrated secondary structure predictions into alignment have shown noteworthy gains in Q-score [27–31].”
• PROMALS3D: a tool for multiple protein sequence and structure alignments (2008, methodology): “For this reason, the Expresso webserver of 3DCoffee restricts the use of homolog3Ds only when they show above 60% sequence identity to the targets.”