Model Building Report

This document lists the results for the homology modelling project "binder" submitted to SWISS-MODEL workspace on July 15, 2025, 1:09 p.m..The submitted primary amino acid sequence is given in Table T1.

If you use any results in your research, please cite the relevant publications:

• Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T
  SWISS-MODEL: homology modelling of protein structures and complexes.
  Nucleic Acids Res 46, W296-W303. (2018) 2978835510.1093/nar/gky427
• Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T
  The SWISS-MODEL Repository - new features and functionality.
  Nucleic Acids Res 45, D313-D319. (2017) 2789967210.1093/nar/gkw1132
• Studer G, Tauriello G, Bienert S, Biasini M, Johner N, Schwede T
  ProMod3 - A versatile homology modelling toolbox.
  PLOS Comp Biol 17(1), e1008667. (2021) 3350798010.1371/journal.pcbi.1008667
• Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T
  QMEANDisCo - distance constraints applied on model quality estimation.
  Bioinformatics 36, 1765-1771. (2020) 3169731210.1093/bioinformatics/btz828
• Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T
  Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
  Scientific Reports 7. (2017) 2887468910.1038/s41598-017-09654-8

Results

The user uploaded a template structure to use for the modelling process.

Models

The following model was built (see Materials and Methods "Model Building"):

Model #01	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.5.0	hetero-1-1-mer	None	0.69	0.71 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
template_upload.1	100.00	hetero-1-1-mer	0.85	HHblits	Unknown	-	0.64	A: 1-136 B: 1-120	1.00	Polypeptide Polypeptide

The template contained no ligands.

Target                   HTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTY
template_upload.1.A      HTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTY

Target                   FYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYV
template_upload.1.A      FYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYV

Target                   SKFSTVPVSHHECSFLKPCLCVSQRS
template_upload.1.A      SKFSTVPVSHHECSFLKPCLCVSQRS

Target                   PPNINDPNNIKEPSEEELKEFEERMKFLIDYLEKHESEHPGEAPEHWTAELSIAM
template_upload.1.B      PPNINDPNNIKEPSEEELKEFEERMKFLIDYLEKHESEHPGEAPEHWTAELSIAM

Target                   VYKTIKEVNPNIDPIEIIKAIEYGHLTKEDIVFPGVTVKFDEDGVPVKIITDDKT
template_upload.1.B      VYKTIKEVNPNIDPIEIIKAIEYGHLTKEDIVFPGVTVKFDEDGVPVKIITDDKT

Target                   IELPEVEKAP
template_upload.1.B      IELPEVEKAP

---

Materials and Methods

Template Selection

For each identified template, the template's quality has been predicted from features of the target-template alignment. The templates with the highest quality have then been selected for model building.

User Template Alignment

The user entered their own target sequence together with an uploaded a template structure file in PDB format.

Model Building

Models are built based on the target-template alignment using ProMod3 (Studer et al.). Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field.

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Studer et al.).

Ligand Modelling

Ligands present in the template structure are transferred by homology to the model when the following criteria are met: (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.

Oligomeric State Conservation

The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.

References

• Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL
  BLAST+: architecture and applications.
  BMC Bioinformatics, 10, 421-430. (2009) 2000350010.1186/1471-2105-10-421
• Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J
  HH-suite3 for fast remote homology detection and deep protein annotation.
  BMC Bioinformatics 20, 473. (2019) 3152111010.1186/s12859-019-3019-7

Table T1:

Primary amino acid sequences for which templates were searched and models were built.

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
template_upload.1	100.00	hetero-1-1-mer	0.85	HHblits	Unknown	NA	0.64	1.00	Polypeptide; Polypeptide