SSTSUM Markov matrix and related parameters :
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SSTSUM matrix at t=1
A stochastic Markov matrix of conditional probabilities for 3 states of secondary structures {coil, strand of β sheet, helix} at 1% expected change. Exponentiate this matrix (Mt ) to derive a stochastic Markov matrix for any time t.
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Expected change of SSTSUM matrix
The expected change of SSTSUM matrix at t = [1, 250].
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Time dependent 3-state alignment machine transition probabilities
Associated time-dependent transition probabilities of {match, insert, delete} alignment machine states for t = [1, 250].
Details of raw data used in the manuscript :
- List of million domain pairs
- List of domain pairs sampled at the same family level
- List of domain pairs sampled at the same superfamily level
- List of domain pairs sampled at the same fold level
- List of domain pairs sampled at the same class level
- List of domain pairs sampled at different decoy level
- List of PDB IDs in the non-redundant dataset (deposited before 2017-01-01) used to search hits in SSTPred
- Benchmark dataset used in the inference of SSTSUM and associated data
Plots and associated raw data :
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Structure time (t3D→2D) vs sequence time (t1D) plots for million domain pairs
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Structure time (t3D→2D) vs sequence time (t1D) plots for 5 distinct groups of domain pairs based on SCOP classification
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Q3 Accuracies of Deep-CNF, PSIPRED, JPred, SSTPred (our predictor) over CASP 14 and CASP 15 targets
Raw data for above plot Raw data for above plot
Supplementary materials :
C++ source codes :
Links to other source codes used :
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SeqMMLigner
SeqMMLigner is a command line program to infer alignments between amino acid sequences.
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SST (web server)
SST is a web server to assign secondary structure to protein coordinate data.
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MMLigner
MMLigner is a command-line program to infer pairwise protein structure alignments.
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TM-align
TM-align is a program to infer pairwise protein structure alignments.
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Dali
Dali is a program to infer pairwise protein structure alignments.