A method for searching for a protein complex structure analog template

Abstract

The application discloses a protein complex structure similar template searching method, which comprises the following steps: firstly, constructing a protein complex template database and a fusion template database; then inputting a single-chain structure of a target protein, searching a global template and a local template in the complex template database, and searching a global template and a local template in the fusion template database again if the searched template is poor; and finally, selecting the best template searched in the two databases as the structure similar template of the target protein. The application provides a protein complex structure similar template searching method with high precision.

Description

Technical Field

[0001] The present invention belongs to the fields of bioinformatics, intelligent optimization and computer application, and in particular relates to a method for searching similar templates of protein complex structures. Background Art

[0002] For most target proteins, sequence alignment or sequencing based on sequence homology or structural similarity is more reliable and the process is more convenient. Especially when the target protein shares significant homology with the template, the prediction results are generally highly reliable. This makes template-based structure prediction methods more popular in practical applications. However, the number of known protein complex structures in the PDB is far less than that of monomeric proteins, resulting in a relatively small number of template structures required for prediction, or even a lack thereof. Both Marsh et al. (Cell) and Pasek et al. (Bioinformatics) pointed out that proteins with multiple domains (i.e., multidomains) are primarily derived from a series of gene fusion and fission events. In other words, most multidomain proteins are formed by the fusion and fission of single chains of protein complexes in the genome. This allows for the reliable inference of interchain information of protein complexes from multidomain proteins. Therefore, a multidomain protein template library can be used as a supplement to the complex template library to construct a library of structurally similar templates, thereby improving the completeness of the database.

[0003] Currently, a variety of template search methods are available. These include homology modeling methods such as SWISS-MODEL developed by the Schwede laboratory and Modeller developed by the Sali laboratory, as well as the threading-based prediction method I-TASSER developed by the Zhang laboratory. Although these methods have achieved significant success, several issues (such as incomplete template databases and low accuracy in searching for redundant and protein complex templates) limit the accuracy and efficiency of existing algorithms. Furthermore, most algorithms require manual processing of intermediate steps, which hinders their use by users in fields outside of structural biology.

[0004] Therefore, existing methods for searching protein complex templates have defects in accuracy and automation and need to be improved. Summary of the Invention

[0005] In order to overcome the shortcomings of existing methods for searching protein complex templates, such as low precision and the need for manual intervention during execution, the present invention provides a method for searching protein complex structure-similar templates with high precision.

[0006] In order to solve the above technical problems, the present invention provides the following technical solutions:

[0007] A method for searching for templates with similar structures in a protein complex, comprising the following steps:

[0008] 1) Input the single-chain structures of the protein complex to be searched;

[0009] 2) Setting parameters: minimum number of single-chain residues N min , sequence similarity coefficient threshold S thresholds , structural similarity coefficient threshold T thresholds , template matching percentage C percentage , template structure similarity threshold G thresholds ;

[0010] 3) constructing a database of complex templates;

[0011] 4) Building a fusion template database;

[0012] 5) Search for similar templates from the complex template database; if the best template found has a score of G score Less than G thresholds , then execute step 6) otherwise this template is the final template;

[0013] 6) Search for similar templates from the fusion template database and compare them with the best template searched in step 5), and take the template with the highest score as the final template.

[0014] Further, the process of 3) is as follows:

[0015] 3.1) All protein complexes were selected from the PDB database;

[0016] 3.2) Remove residues with a number less than N in each complex min single chain;

[0017] 3.3) removing single chains in each complex that have no contact with other chains;

[0018] 3.4) According to sequence similarity S thresholds CD-HIT was used to remove redundant proteins;

[0019] 3.5) Use USalign to remove structural similarity TM-score greater than T thresholds protein complexes;

[0020] 3.6) All single-chain structures in the database are removed again.

[0021] Furthermore, the process of 4) is as follows:

[0022] 4.1) All multidomain proteins were selected from the PDB database;

[0023] 4.2) According to sequence similarity S thresholds CD-HIT was used to remove redundant proteins;

[0024] 4.3) Use CD-HIT to sort the remaining proteins in CATH and SCOPe that have sequence similarity less than S thresholds The multi-domain proteins were added to the database;

[0025] 4.4) Use TMalign to align sequences with similarity greater than S in PDB, CATH, and SCOPe. thresholds But TM-score is smaller than T thresholds The multi-domain proteins were added to the database.

[0026] Furthermore, the process of 5) is as follows:

[0027] 5.1) Searching for global templates: Use TM-align to align each chain in the complex template database. After each chain is aligned, remove the matched residues in the template and then match the next chain. Record the percentage of the number of matched residues in each chain to the total number of residues in that chain. If the matching percentage is greater than C percentage , then the chain is considered to have been matched by the template, and the templates that all chains match are screened out, and G is selected score The highest template is used as the global template, where G score The calculation formula is as follows:

[0028]

[0029] N chain The number of all single chains in the input complex structure, TM-score d is the TM-score of the d-th chain;

[0030] 5.2) Searching for local templates: If the template cannot cover all chains, then according to the sliding window process, the global templates of each two adjacent chains are searched in the complex template database for these two chains in turn. Then, the global templates corresponding to each group of different chain numbers are connected with the same chain number as the reference to obtain the local template of the complex;

[0031] 5.3) Determine the best local template and the corresponding G of the global template score With G thresholds Compare, if greater than G thresholds , the template with the higher score is the final template of the complex, otherwise go to step 6).

[0032] The technical concept of the present invention is as follows: first, a protein complex template database and a fusion template database are constructed; then, the single-chain structure of the target protein is input, and this structure is searched for global templates and local templates in the complex template database. If the quality of the searched template is poor, the global template and local template are searched again in the fusion template library; finally, the best template searched in the two databases is selected as the structurally similar template of the target protein.

[0033] The beneficial effects of the present invention are as follows: using multi-domain protein data as a supplement to construct a structure-similar template library to improve the integrity of the database; and using two methods of searching global templates and local templates to improve the accuracy of searching templates. BRIEF DESCRIPTION OF THE DRAWINGS

[0034] Figure 1 This is the basic flow chart of this method.

[0035] Figure 2 This is a flowchart for constructing a complex template database.

[0036] Figure 3 It is a flow chart for building a fusion template database.

[0037] Figure 4 They are two single chains of the protein complex 3R8I.

[0038] Figure 5 This is the best complex template 2I4J found by this method. DETAILED DESCRIPTION

[0039] The present invention will be further described below with reference to the accompanying drawings.

[0040] Reference Figures 1 to 5 , a method for searching for templates similar to protein complex structures, comprising the following steps:

[0041] 1) Input the single-chain structures of the protein complex to be searched;

[0042] 2) Setting parameters: minimum number of single-chain residues N min , sequence similarity coefficient threshold S thresholds , structural similarity coefficient threshold T thresholds , template matching percentage C percentage , template structure similarity threshold G thresholds ;

[0043] 3) Constructing a complex template database, the process is as follows:

[0044] 3.1) All protein complexes were selected from the PDB database;

[0045] 3.2) Remove residues with a number less than N in each complexmin single chain;

[0046] 3.3) removing single chains in each complex that have no contact with other chains;

[0047] 3.4) According to sequence similarity S thresholds CD-HIT (https: / / github.com / weizhongli / cdhit / releases) was used to remove redundant proteins;

[0048] 3.5) Use USalign (https: / / zhanggroup.org / US-align / ) to remove structural similarity TM-

[0049] score is greater than T thresholds protein complexes;

[0050] 3.6) Remove all single-chain structures from the database again;

[0051] 4) Build a fusion template database. The process is as follows:

[0052] 4.1) All multidomain proteins were selected from the PDB database;

[0053] 4.2) According to sequence similarity S thresholds CD-HIT (https: / / github.com / weizhongli / cdhit / releases) was used to remove redundant proteins;

[0054] 4.3) Use CD-HIT (https: / / github.com / weizhongli / cdhit / releases) to compare the protein sequences in CATH and SCOPe with those in 4.2) that are less similar than S thresholds The multi-domain proteins were added to the database;

[0055] 4.4) Use TMalign (https: / / zhanggroup.org / TM-align / ) to align sequences with similarity greater than S in PDB, CATH, and SCOPe. thresholds But TM-score is smaller than T thresholds The multi-domain proteins were added to the database;

[0056] 5) Search for similar templates from the complex template database; if the best template found has a score of G score Less than G thresholds , then execute step 6) Otherwise, this template is the final template; the process is as follows:

[0057] 5.1) Search for global template: Each chain is aligned in the complex template database using TM-align (https: / / zhanggroup.org / TM-align / ). After each chain is aligned, the matched residues are removed from the template and then the next chain is matched. The percentage of the number of matched residues in each chain is recorded. If the matching percentage is greater than C percentage , then the chain is considered to have been matched by the template, and the templates that all chains match are screened out, and G is selected score The highest template is used as the global template, where G score The calculation formula is as follows:

[0058]

[0059] N chain The number of all single chains in the input complex structure, TM-score d is the TM-score of the d-th chain;

[0060] 5.2) Finding a local template: If the template does not cover all chains, then, using a sliding window process, the global templates of each pair of adjacent chains are searched in the complex template database. The global templates corresponding to each set of different chain numbers are then connected using the same chain number as the reference to obtain the local template of the complex. For example, if the input is three chains (chain A, chain B, chain C), the database is first searched for a global template AB that covers chains A and B, and a global template BC that covers chains B and C. Then, based on the alignment of chain B, the two templates AB and BC are connected to obtain the local template ABC of the three chains.

[0061] 5.3) Determine the best local template and the corresponding G of the global template score With G thresholds Compare, if greater than G thresholds , the template with the highest score is the final template of the complex, otherwise go to step 6);

[0062] 6) Search for similar templates from the fusion template database and compare them with the best template searched in step 5), and take the template with the highest score as the final template.

[0063] This embodiment includes two single chains in the protein complex 3R8I as an embodiment, and provides a method for searching for templates with similar structures in protein complexes, the method comprising the following steps:

[0064] 1) Input the single-chain structures of the protein complex to be searched;

[0065] 2) Setting parameters: minimum number of single-chain residues N min =30, sequence similarity coefficient threshold Sthresholds =70%, structural similarity coefficient threshold T thresholds =0.5, template matching percentage C percentage = 60%, template structure similarity threshold G thresholds＝ 0.65;

[0066] 3) Constructing a complex template database, the process is as follows:

[0067] 3.1) All protein complexes were selected from the PDB database;

[0068] 3.2) Remove residues with a number less than N in each complex min single chain;

[0069] 3.3) removing single chains in each complex that have no contact with other chains;

[0070] 3.4) According to sequence similarity S thresholds CD-HIT (https: / / github.com / weizhongli / cdhit / releases) was used to remove redundant proteins;

[0071] 3.5) Use USalign (https: / / zhanggroup.org / US-align / ) to remove structural similarity TM-

[0072] score is greater than T thresholds protein complexes;

[0073] 3.6) Remove all single-chain structures from the database again;

[0074] 4) Build a fusion template database. The process is as follows:

[0075] 4.1) All multidomain proteins were selected from the PDB database;

[0076] 4.2) According to sequence similarity S thresholds CD-HIT (https: / / github.com / weizhongli / cdhit / releases) was used to remove redundant proteins;

[0077] 4.3) Use CD-HIT to sort the remaining proteins in CATH and SCOPe that have sequence similarity less than S thresholds The multi-domain proteins were added to the database;

[0078] 4.4) Use TMalign (https: / / zhanggroup.org / TM-align / ) to align sequences with similarity greater than S in PDB, CATH, and SCOPe. thresholdsBut TM-score is smaller than T thresholds The multi-domain proteins were added to the database;

[0079] 5) Search for similar templates from the complex template database; if the best template found has a score of G score Less than G thresholds , then execute step 6) Otherwise, this template is the final template; the process is as follows:

[0080] 5.1) Find global template: Use TM-align to align each chain in the complex template database

[0081] (https: / / zhanggroup.org / TM-align / ) for alignment. After each chain is aligned, the matched residues are removed from the template and then the next chain is matched. The percentage of the number of matched residues in each chain to the total number of residues in the chain is recorded. If the matching percentage is greater than C percentage , then the chain is considered to have been matched by the template, and the templates that all chains match are screened out, and G is selected score The highest template is used as the global template, where G score The calculation formula is as follows:

[0082]

[0083] N chain The number of all single chains in the input complex structure, TM-score d is the TM-score of the d-th chain;

[0084] 5.2) Searching for local templates: If the template cannot cover all chains, then according to the sliding window process, the global templates of each two adjacent chains are searched in the complex template database for these two chains in turn. Then, the global templates corresponding to each group of different chain numbers are connected with the same chain number as the reference to obtain the local template of the complex;

[0085] 5.3) Determine the best local template and the corresponding G of the global template score With G thresholds Compare, if greater than G thresholds , the template with the highest score is the final template of the complex, otherwise go to step 6);

[0086] 6) Search for similar templates from the fusion template database and compare them with the best template searched in step 5), and take the template with the highest score as the final template.

[0087] This example takes two single chains in the protein complex 3R8I as an example. The two single chain structures are as follows. Figure 4 As shown, the complex template structure 2I4J obtained by searching according to this method is as follows Figure 5 shown.

[0088] The above description is the search result obtained by the present invention using two single chains in the protein complex 3R8I as an example, and does not limit the scope of implementation of the present invention. Various modifications and improvements made thereto without departing from the scope of the basic content of the present invention should not be excluded from the scope of protection of the present invention.

Claims

1. A method for searching for templates similar to protein complex structures, characterized in that: The method comprises the following steps: 1) Input the single-chain structures of the protein complex to be searched; 2) Setting parameters: minimum number of single-chain residues N min , sequence similarity coefficient threshold S thresholds , structural similarity coefficient threshold T thresholds , template matching percentage C percentage , template structure similarity threshold G thresholds ; 3) Constructing a complex template database, the process is as follows: 3.1) All protein complexes were selected from the PDB database; 3.2) Remove residues with a number less than N in each complex min single chain; 3.3) removing single chains in each complex that have no contact with other chains; 3.4) According to sequence similarity S thresholds CD-HIT was used to remove redundant proteins; 3.5) Use USalign to remove structural similarity TM-score greater than T thresholds protein complexes; 3.6) Remove all single-chain structures from the database again; 4) Build a fusion template database. The process is as follows: 4.1) All multidomain proteins were selected from the PDB database; 4.2) According to sequence similarity S thresholds CD-HIT was used to remove redundant proteins; 4.3) Use CD-HIT to sort the remaining proteins in CATH and SCOPe that have sequence similarity less than S thresholds The multi-domain proteins were added to the database; 4.4) Use TMalign to align sequences with similarity greater than S in PDB, CATH, and SCOPe. thresholds But TM-score is smaller than T thresholds Multidomain proteins added to the database 5) Search for similar templates from the complex template database using both global and local template searches; if the best template found has a score of G score Less than G thresholds , then execute step 6) otherwise this template is the final template; 6) Search for similar templates from the fusion template database and compare them with the best template searched in step 5), and take the template with the highest score as the final template.

2. The method for searching for templates similar to protein complex structures according to claim 1, wherein: The process of 5) is as follows: 5.1) Searching for global templates: Use TM-align to align each chain in the complex template database. After each chain is aligned, remove the matched residues in the template and then match the next chain. Record the percentage of the number of matched residues in each chain to the total number of residues in that chain. If the matching percentage is greater than C percentage , then the chain is considered to have been matched by the template, and the templates that all chains match are screened out, and G is selected score The highest template is used as the global template, where G score The calculation formula is as follows: N chain The number of all single chains in the input complex structure, TM-score d is the TM-score of the d-th chain; 5.2) Searching for local templates: If the template cannot cover all chains, then according to the sliding window process, the global templates of each two adjacent chains are searched in the complex template database for these two chains in turn. Then, the global templates corresponding to each group of different chain numbers are connected with the same chain number as the reference to obtain the local template of the complex; 5.3) Determine the best local template and the corresponding G of the global template score With G thresholds Compare, if greater than G thresholds , the template with the higher score is the final template of the complex, otherwise go to step 6).

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