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tmtools - Structural superposition

The tmtools module provides access to the structural superposition programs TMscore, Tmalign and MMalign developed by Y. Zhang and J. Skolnick. These programs superpose a model onto a reference structure, using the positions of the Calpha atoms only. While at their core, these programs essentially use the same algorithm, they differ on how the Calphas are paired. TMscore pairs the Calpha atom based on the residue number, TMalign calculates an optimal pairing of Calpha atom based on heuristics.

Citation:

Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9

Distance measures used by TMscore

There are many different ways to describe the structural similarity of two protein structures at the Calpha level. TMscore calculate several of these measures. The most common is to describe the difference in terms of the root mean square deviation of the Calpha positions, the RMSD. Despite its common use, RMSD has several drawbacks when working with incomplete models. Since the RMSD highly depends on the set of included atoms, it is relatively easy to obtain a smaller RMSD by omitting flexible parts of a protein structure. This has lead to the introduction of the global distance test (GDT). A model is compared to a reference by calculating the fraction of Calpha atoms that can be superposed below a certain cutoff, e.g. 1Å. The fractions of several such cutoffs are combined into the GDT_TS (1, 2, 4 and 8Å) and GDT_HA (0.5, 1, 2, 4Å) and divided by four to obtain the final measure. In contrast to RSMD, GDT is an agreement measure. The higher the value, the more similar the two structures are. TM-score (not to be confused by TMscore, the program), additionally adds a size dependences to the GDT measure by taking the protein length into account. As with GDT, the bigger the value, the more similar the two structures are.

Common Usage

The following example shows how to use TMscore to superpose two protein structures and print the RMSD as well as the GDT_TS and GDT_HA similarity measures.

from ost.bindings import tmtools

pdb1=io.LoadPDB('1ake.pdb', restrict_chains='A')
pdb2=io.LoadPDB('4ake.pdb', restrict_chains='A')
result=tmtools.TMScore(pdb1, pdb2)
print result.rmsd_below_five # 1.9
print result.gdt_ha # 0.41
print result.gdt_ts # 0.56

Usage of TMalign

TMAlign(model1, model2, tmalign=None)

Performs a sequence independent superposition of model1 onto model2, the reference.

Parameters:
  • model1 (EntityView or EntityHandle) – The model structure. If the superposition is successful, will be superposed onto the reference structure
  • model2 (EntityView or EntityHandle) – The reference structure
  • tmalign – If not None, the path to the tmalign executable.
Returns:

The result of the tmscore superposition

Return type:

TMAlignResult

Raises:

FileNotFound if tmalign could not be located.

Raises:

RuntimeError if the superposition failed

class TMAlignResult(rmsd, tm_score, aligned_length, transform, ref_sequence, alignment)

Holds the result of running TMalign

rmsd

The RMSD of the common Calpha atoms of both structures

transform

The transform that superposes the model onto the reference structure.

Type:Mat4
alignment

The alignment of the structures, that is the pairing of Calphas of both structures. Since the programs only read ATOM records, residues consisting of HETATMs (MSE) are not included in the alignment.

Type:AlignmentHandle
tm_score

The TM-score of the structural superposition

Usage of TMscore

TMScore(model1, model2, tmscore=None)

Performs a sequence dependent superposition of model1 onto model2, the reference.

Parameters:
  • model1 (EntityView or EntityHandle) – The model structure. If the superposition is successful, will be superposed onto the reference structure
  • model2 (EntityView or EntityHandle) – The reference structure
  • tmscore – If not None, the path to the tmscore executable.
Returns:

The result of the tmscore superposition

Return type:

TMScoreResult

Raises:

FileNotFound if tmalign could not be located.

Raises:

RuntimeError if the superposition failed

class TMScoreResult(rmsd_common, tm_score, max_sub, gdt_ts, gdt_ha, rmsd_below_five, transform)

Holds the result of running TMscore

rmsd_common

The RMSD of the common Calpha atoms of both structures

rmsd_below_five

The RMSD of all Calpha atoms that can be superposed below five Angstroem

tm_score

The TM-score of the structural superposition

transform

The transform that superposes the model onto the reference structure.

Type:Mat4
gdt_ha

The GDT_HA of the model to the reference structure.

gdt_ts

The GDT_TS of the model to the reference structure.

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