SAM-T08, HMM-based protein structure prediction
By Kevin J. Karplus. 2009
140 citations recorded by the source corpus.
The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue–residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html
Subfields: Materials Chemistry, Molecular Biology
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
- Andriy Kryshtafovych
- Yang Zhang
- Krzysztof Fidelis
- Bohdan Monastyrskyy
- Anna Tramontano
- David Baker
- Torsten Schwede
- Lukasz Kurgan
In Molecular Biology
- Yang Zhang
- Andriy Kryshtafovych
- David Baker
- Torsten Schwede
- Krzysztof Fidelis
- Bohdan Monastyrskyy
- Anna Tramontano
- Jinbo Xu
Citations in the corpus
- New encouraging developments in contact prediction: assessment of the CASP11 results (2015, methodology): “A good candidate for the reference method is the SAM-T08-server, 47 which has been participating in CASP since CASP8 (2008), and whose methodology did not change since.”
- Evaluation of residue-residue contact prediction in CASP10 (2013, methodology): “These methods use neural networks 23–29 , support vector machines 30–32 , hidden Markov models 33–35 , genetic algorithms 36 , random forest models 37 , and learning classifier systems 38 .”
- Protein sequence comparison and fold recognition: progress and good-practice benchmarking. (2011, background): “Other scores that have become widely used recently are predicted solvent accessibility, predicted number of tertiary residue–residue contacts (coordination number) [12, 18, 19, 20 , 21], and 1D environmental fitness scores [22], which evaluate how well the amino acid distribution at each query posit”
- Computational prediction of secondary and supersecondary structures. (2013, methodology): “We note that only a few methods, including SSpro8 (115) and SAM-T08 (101), predict the 8-state secondary structure.”
- Generalized Fragment Picking in Rosetta: Design, Protocols and Applications (2011, background): “Taking into account the shares of the three predictors defined as in quota.def file listed above, one would expect 200 * 0.1 = 20 helical fragments: 12 from PsiPred, 4 from SAM and 4 from Jufo.”