ArticleProtein engineering, design & selection : PEDS2009
Alignment of multiple protein structures based on sequence and structure features.
Article in Protein engineering, design & selection : PEDS, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy.Genome biology and evolution · 2020Article
- Benchmarking Methods of Protein Structure Alignment.Journal of molecular evolution · 2020Article
- mTM-align: an algorithm for fast and accurate multiple protein structure alignment.Bioinformatics (Oxford, England) · 2018Article
- Characterization of SPP inhibitors suppressing propagation of HCV and protozoa.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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- Discovery of novel non-competitive inhibitors of mammalian neutral M1 aminopeptidase (APN).Biochimie · 2017Article
- PSSweb: protein structural statistics web server.Nucleic acids research · 2016Article
- Comparative Protein Structure Modeling Using MODELLER.Current protocols in bioinformatics · 2016Article
- Molecular characterization of a cathepsin F-like protease in Trichinella spiralis.Parasites & vectors · 2015Article
- HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA.Biomolecules · 2015Article
- Identification of Tyr residues that enhance folate substrate binding and constrain oscillation of the proton-coupled folate transporter (PCFT-SLC46A1).American journal of physiology. Cell physiology · 2015Article
- Consequences of domain insertion on sequence-structure divergence in a superfold.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- SLC classification: an update.Clinical pharmacology and therapeutics · 2013Article
- Role of the fourth transmembrane domain in proton-coupled folate transporter function as assessed by the substituted cysteine accessibility method.American journal of physiology. Cell physiology · 2013Article
- Molecular modeling and ligand docking for solute carrier (SLC) transporters.Current topics in medicinal chemistry · 2013Review
- Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator.Intrinsically disordered proteins · 2013Article
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5 authors.
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Abstract
Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue type, residue position, residue accessible surface area, residue secondary structure state and the conformation of a short segment centered on the residue. The multiple alignment is built by following the 'guide' tree constructed from the matrix of all pairwise protein alignment scores. Importantly, the method does not depend on the exact values of various parameters, such as feature weights and gap penalties, because the optimal alignment across a range of parameter values is found. Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments. On the average, SALIGN produces a 15% improvement in structural overlap over HOMSTRAD and 14% over MUSTANG, and yields more equivalent structural positions than TM-align and CE in 90% and 95% of cases, respectively. The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling.
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