Delaunay‐based nonlocal interactions are sufficient and accurate in protein fold recognition

Mirzaie, Mehdi; Sadeghi, Mehdi

doi:10.1002/prot.24407

Cited by 7 publications

(6 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fact, the first attempt to employ contact areas as a foundation for knowledge‐based potentials was made over a decade ago by McConkey et al Contact areas in both CAD‐score and the McConkey method are derived from variants of the Voronoi tessellation. Voronoi and related tessellation methods proved to be an effective means in the analysis of various structural features, including the identification of physical contacts that could be utilized in deriving distance‐based statistical potentials . However, to the best of our knowledge, the study by McConkey et al so far has been the only QA method based on tessellation‐derived contact areas.…”

Section: Introductionmentioning

confidence: 99%

“…Voronoi and related tessellation methods proved to be an effective means in the analysis of various structural features, 19-23 including the identification of physical contacts that could be utilized in deriving distance-based statistical potentials. [24][25][26] However, to the best of our knowledge, the study by McConkey et al so far has been the only QA method based on tessellation-derived contact areas. Their method achieved respectable results in discriminating native protein structures from decoys; however, perhaps mainly due to the lack of publicly available software implementations, the prospects of applying contact areas for the assessment of protein structural models remained largely unexplored.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

VoroMQA: Assessment of protein structure quality using interatomic contact areas

2017

View full text Add to dashboard Cite

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation-based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single-model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131-1145. © 2017 Wiley Periodicals, Inc.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

VoroMQA: Assessment of protein structure quality using interatomic contact areas

2017

View full text Add to dashboard Cite

show abstract

“…The energy functions for assessment of protein structure extracted in TOP500H records as described in our previous study . TOP500H contains 500 nonredundant proteins with resolution of at least 1.8 Å.…”

Section: Methodsmentioning

confidence: 99%

“…Knowledge‐based potentials (KBP) are one type of the energy functions which derived from databases of known protein conformations. They are derived from a non‐redundant set of protein X‐ray structures by measuring the probability of a special feature such as distance, relative to a reference state . Conversion of probability into an energy function is normally done by employing Boltzmann's law .…”

Section: Introductionmentioning

confidence: 99%

“…In the previous study, we introduced a KBP and showed that considering only non‐local interactions (interactions of two atoms within residues with a sequence separation larger than five amino acids) extracted using Delaunay tessellation are accurate and sufficient for protein fold recognition. Here, in order to clarify the role of hydrophobic amino acids in identification of protein native structure, we calculated only pairwise energies between amino acids with hydrophobic side chains PHE (F), LEU (L), VAL (V), ILE (I), ALA (A), TRP (W) and TYR (Y).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Hydrophobic residues can identify native protein structures

Mirzaie

2018

Proteins

Self Cite

View full text Add to dashboard Cite

Evaluation of protein structures needs a trustworthy potential function. Although several knowledge-based potential functions exist, the impact of different types of amino acids in the scoring functions has not been studied yet. Previously, we have reported the importance of nonlocal interactions in scoring function (based on Delaunay tessellation) in discrimination of native structures. Then, we have questioned the structural impact of hydrophobic amino acids in protein fold recognition. Therefore, a Hydrophobic Reduced Model (HRM) was designed to reduce protein structure of FS (Full Structure) into RS (Reduced Structure). RS is considered as a reduced structure of only seven hydrophobic amino acids (L, V, F, I, A, W, Y) and all their interactions. The presented model was evaluated via four different performance metrics including the number of correctly identified natives, the Z-score of the native energy, the RMSD of the minimum score, and the Pearson correlation coefficient between the energy and the model quality. Results indicated that only nonlocal interactions between hydrophobic amino acids could be sufficient and accurate enough for protein fold recognition. Interestingly, the results of HRM is significantly close to the model that considers all amino acids (20-amino acid model) to discriminate the native structure of the proteins on eleven decoy sets. This indicates that the power of knowledge-based potential functions in protein fold recognition is mostly due to hydrophobic interactions. Hence, we suggest combining a different well-designed scoring function for non-hydrophobic interactions with HRM to achieve better performance in fold recognition.

show abstract

Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures

Mirzaie

2019

Amino Acids

View full text Add to dashboard Cite

Delaunay‐based nonlocal interactions are sufficient and accurate in protein fold recognition

Cited by 7 publications

References 62 publications

VoroMQA: Assessment of protein structure quality using interatomic contact areas

VoroMQA: Assessment of protein structure quality using interatomic contact areas

Hydrophobic residues can identify native protein structures

Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures

Contact Info

Product

Resources

About