MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information
Explore this paper's citation graph
Summary
A new threading algorithm MUSTER is developed by extending the previous sequence profile–profile alignment method, PPA, which shows a better performance than using the conventional optimization methods based on the PROSUP database.
- Type
- article
- Published
- 2008-08-01
- Cited by
- 392
- References
- 66
- Access
- Open access
- OpenAlex
- https://openalex.org/W1978304263
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:16425690
Keywords
Threading (protein sequence), Computer science, Sequence alignment, Multiple sequence alignment, Structural alignment
References
- Critical assessment of methods of protein structure prediction (CASP)‐round V
- The PyMOL Molecular Graphics System
- Position-based sequence weights.
- Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences
- A simple method for displaying the hydropathic character of a protein.
- A study of combined structure/sequence profiles.
- Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.
- Assessment of predictions submitted for the CASP6 comparative modeling category
- FFAS03: a server for profile–profile sequence alignments
- FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
- Residue depth: a novel parameter for the analysis of protein structure and stability.
- LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction
- Automated server predictions in CASP7
- A new approach to protein fold recognition
- Topology fingerprint approach to the inverse protein folding problem.
- Alignment of protein sequences by their profiles
- Automated structure prediction of weakly homologous proteins on a genomic scale.
- Ab initio protein structure prediction using chunk-TASSER.
- Prediction of protein antigenic determinants from amino acid sequences.
Cited by
- HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition
- CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
- Sisters Unbound Is Required for Meiotic Centromeric Cohesion in Drosophila melanogaster
- Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest
- In silico analysis of functional nsSNPs in human TRPC6 gene associated with steroid resistant nephrotic syndrome.
- Inducible gene expression system by 3-hydroxypropionic acid
- Recent advances in sequence-based protein structure prediction
- Bioinformatics : Tools and Applications
- UNDERSTANDING THE MEIOTIC ROLES OF SISTERS UNBOUND IN DROSOPHILA MELANOGASTER
- Molecular Modelling of Multi-Drug Resistance Transporters
- Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking.
- Isolation and in silico depiction of novel R2-R3 MYB transcription factors from sugarcane.
- A Kazal-Type Serine Protease Inhibitor from the Defense Gland Secretion of the Subterranean Termite Coptotermes formosanus Shiraki
- The 3D model of the lipase/acyltransferase from Candida parapsilosis, a tool for the elucidation of structural determinants in CAL-A lipase superfamily.
- Current Advances in the Identification and Characterization of Putative Drug and Vaccine Targets in the Bacterial Genomes.
- Protein function prediction by integrating sequence, structure and binding affinity information
- Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment
- Boosting Protein Threading Accuracy
- Proteína LIC10494 de Leptospira interrogans serovar Copenhageni:modelo estructural y regiones funcionales asociadas
- Comparative Protein Structure Modeling Using Modeller
Related papers
- ALIGN_MTX - An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment
- Alignment of protein sequences by their profiles
- Homology-extended sequence alignment
- Optimization of multiple‐sequence alignment based on multiple‐structure alignment
- A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites
- Confidence Measures for Fold Recognition
- Protein Threading Based on Multiple Protein Structure Alignment.
- Protein threading using context-specific alignment potential