A simple method for finding a protein’s ligand-binding pockets

Fathi, Seyed Majid Saberi; Tuszyński, Jack A.

doi:10.1186/1472-6807-14-18

Cited by 20 publications

(19 citation statements)

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“…Asp was the most frequent single amino acid with 9 repetitions at the furin active site. This amino acid residue was mainly involved in the interactions as a hydrogen bond acceptor where polar interactions were especially favourable for complex protein-ligand stability [ 40 ]. Asp was also an acidic part of the so-called “classical” catalytic triad, three coordinated amino acids (together with Ser and His) which generated a charge-relay system for activating a nucleophilic attack on enzyme substrate.…”

Section: Discussionmentioning

confidence: 99%

Computational study of pomegranate peel extract polyphenols as potential inhibitors of SARS-CoV-2 virus internalization

et al. 2020

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The search for effective coronavirus disease (COVID-19) therapy has attracted a great deal of scientific interest due to its unprecedented health care system overload worldwide. We have carried out a study to investigate the in silico effects of the most abundant pomegranate peel extract constituents on the multi-step process of serious acute respiratory syndrome coronavirus 2 (SARS-CoV-2) internalization in the host cells. Binding affinities and interactions of ellagic acid, gallic acid, punicalagin and punicalin were studied on four selected protein targets with a significant and confirmed role in the process of the entry of virus into a host cell. The protein targets used in this study were: SARS-CoV-2 spike glycoprotein, angiotensin-converting enzyme 2, furin and transmembrane serine protease 2. The results showed that the constituents of pomegranate peel extracts, namely punicalagin and punicalin had very promising potential for significant interactions with the selected protein targets and were therefore deemed good candidates for further in vitro and in vivo evaluation.

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Section: Discussionmentioning

confidence: 99%

Computational study of pomegranate peel extract polyphenols as potential inhibitors of SARS-CoV-2 virus internalization

et al. 2020

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“… 66 . It can also be applied to search for a specific interface among a set of candidate interfaces on a protein’s surface, for example – for searching a DNA and RNA binding interfaces, given a set of candidate binding interfaces on a protein surface, or for searching a ligand binding interface from a list of potential interfaces given by a pocket prediction tool, such as CASTp 35 . By allowing a fast, sequence- and fold- independent search in large datasets of functional surfaces, PatchBag can boost the current comprehension of protein function, and reveal novel evolutionary relationships between protein surfaces and interfaces, which are yet unidentified due to lack of sufficient and efficient computational tools for surface comparisons.…”

Section: Discussionmentioning

confidence: 99%

A Novel Geometry-Based Approach to Infer Protein Interface Similarity

Budowski-Tal

Kolodny

Mandel-Gutfreund

2018

Sci Rep

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The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag – a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.

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“…Note that using this heuristic approach significantly reduces the complexity by avoiding a costly backtracking algorithm. In addition to PocketAlign [30], PocketFEATURE [77] and SiteEngine [69] assigned to this group, geometric hashing and sorting are employed by many other programs to find ligand-binding sites on protein surfaces [78], quantify the similarity between binding pockets [68] and classify functional sites in proteins [79].…”

Section: Group Iv: Methods Employing Geometric Hashing and Sortingmentioning

confidence: 99%

Binding site matching in rational drug design: algorithms and applications

Naderi

Lemoine

Govindaraj

et al. 2018

Briefings in Bioinformatics

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Interactions between proteins and small molecules are critical for biological functions. These interactions often occur in small cavities within protein structures, known as ligand-binding pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational methods including various techniques to represent and compare small molecules as well as local protein structures. In this review, we survey 12 tools widely used to match pockets. These methods are divided into five categories based on the algorithm implemented to construct binding-site alignments. In addition to the comprehensive analysis of their algorithms, test sets and the performance of each method are described. We also discuss general pharmacological applications of computational pocket matching in drug repurposing, polypharmacology and side effects. Reflecting on the importance of these techniques in drug discovery, in the end, we elaborate on the development of more accurate meta-predictors, the incorporation of protein flexibility and the integration of powerful artificial intelligence technologies such as deep learning.

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A simple method for finding a protein’s ligand-binding pockets

Cited by 20 publications

References 50 publications

Computational study of pomegranate peel extract polyphenols as potential inhibitors of SARS-CoV-2 virus internalization

Computational study of pomegranate peel extract polyphenols as potential inhibitors of SARS-CoV-2 virus internalization

A Novel Geometry-Based Approach to Infer Protein Interface Similarity

Binding site matching in rational drug design: algorithms and applications

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