Benchmarking of different molecular docking methods for protein-peptide docking

Agrawal, Piyush; Singh, Harinder; Srivastava, H. K.; Singh, Sandeep; Kishore, G. Indira; Raghava, Gajendra P. S.

doi:10.1186/s12859-018-2449-y

Cited by 108 publications

(87 citation statements)

References 89 publications

(106 reference statements)

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“…A web-based docking tool (PATCHDOCK) was used to study the mode of action of CHEK1 regulation by microRNAs in solid tumors. The PATCHDOCK method is based on the shape complementarity theory [45]. Criteria, such as strong hydrophobic amino acids together with aromatic amino acids, are important to binding interactions in terms of the stability between protein receptors and their ligands.…”

Section: Molecular Docking Analysismentioning

confidence: 99%

Gene Expression Alterations and Molecular Analysis of CHEK1 in Solid Tumors

Fadaka

Bakare

Sibuyi

et al. 2020

Cancers

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Alterations in the Checkpoint kinase (CHEK1) gene, its regulation, and the possible clinical outcomes in human solid tumors have not been previously examined. Therefore, the present study was carried out to evaluate the expression of CHEK1 in solid tumors as well as the mechanism by which it can be regulated through non-coding RNAs. The expression of CHEK1 was investigated using Oncomine analysis. cBioPortal, Kaplan–Meier Plotter, and PrognoScan were performed to identify the prognostic roles of this gene in solid tumors. The copy number alteration, mutation, interactive analysis, and visualization of the altered networks were performed by cBioPortal. The molecular binding analysis was carried out by Schrodinger suite, PATCHDOCK, and discovery studio visualizer. The study demonstrated that the CHEK1 gene was differentially expressed in four different cancers, and that reduced CHEK1 mRNA expression is an unfavorable prognostic factor for patients with gastric and colorectal cancer. The molecular docking results showed that the CHEK1 gene can be regulated by microRNAs (miR-195-5p) due to the number of stable hydrogen atoms observed within the distance of 2.0 Å and the favorable amino acids (Ala221, Ile353, Ile365, Ile756, Val797, Val70, Val154, Ile159, Val347, Tyr804, Phe811, Tyr815, and Phe156) identified in the binding pocket of the argonaute protein. Due to the possibility of CHEK1’s involvement in solid tumors, it may potentially be a target for therapeutic intervention in cancer. Further studies into the interaction between CHEK1 and other co-expressed genes may give further insight into other modes of regulation of this gene in cancer patients.

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Section: Molecular Docking Analysismentioning

confidence: 99%

Gene Expression Alterations and Molecular Analysis of CHEK1 in Solid Tumors

Fadaka

Bakare

Sibuyi

et al. 2020

Cancers

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“…Protein-ligand docking and visualization. Protein and ligand interactions were performed by docking using Hex 8.0.0 (blind docking) to determine the position of brazilin that can bind which PR region, without limiting the possibility to bind outside the binding site [14] [15]. It has an efficiency algorithm to calculate the amount of intermolecular energy from atomic and electrostatic desolvation energy as a correlation function for all configurations and calculate protein-ligand docking by utilizing the Spherical Polar Fourier correlation (SPF) to speed up the calculation and one of the few docking programs that have been built in the graph to see its effect [16] [17].…”

Section: Methodsmentioning

confidence: 99%

Virtual Inhibition Analysis of Bioactive Compound Brazilin (Caesalpinia sappan L.) Toward Progesterone Receptor or Lonaprisan in Breast Cancer Proliferation

Harnis

Hasan²,

Janah³

et al. 2020

Biotropika

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Breast cancer is one of the leading causes of death worldwide. The pathway of breast cancer in KEGG shows that the most effective pathway is through the progesterone receptor (PR). Brazilin is a bioactive compound of secang (Caesalpinia sappan L.) used to inhibit breast cancer through survivin and Bcl-2 pathway but the interaction with PR route is unknown. This research was conducted to determine the virtual interaction between brazilin and PR and its comparison with lonaprisan, so the potential of breast cancer drugs that can overcome through three targets at once with minimal side effects is expected to be known. There are five docking interactions, including the interaction of PRprogesterone, PR-brazilin, PR-brazilin-progesterone, PR-lonaprisan, and PRlonaprisan-progesterone. Protein and ligand preparation was performed by using Discovery Studio Client 2019 and PyRx 0.8, molecular docking was performed by using Hex 8.0.0 and visualization used Discovery Studio Client 2019. Virtual interaction results shows that lonaprisan has the most stable bond (lowest binding energy),-333.8kJ/mol but when progesterone was docked afterwards the result shows the opposite. Brazilin has a more stable bond compared to lonaprisan with a difference of 2.1kJ/mol and supported by hydrophobic bonds also capable of changing the position of progesterone in binding to PR so that it is estimated that brazilin has the potential as SPRMs, an alternative breast cancer drug to replace lonaprisan. Herbal medicine with brazilin can be estimated to fight breast cancer through 3 targets at once (survivin, Bcl-2, PR).

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“…For peptide-based therapeutics, it is important to know their exact binding sites on target proteins, using protein-peptide docking. As the majority of computational docking methods have been developed for drug-protein interactions, Agarwal et al [ 25 ] have carried out extensive benchmarking of six most commonly used methods for a large number of protein-peptide combinations. They report that FRODOCK performed best in case of blind docking and ZDOCK in case of re-docking.…”

Section: Structural Bioinformaticsmentioning

confidence: 99%

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

et al. 2019

Self Cite

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InCoB, one of the largest annual bioinformatics conferences in the Asia-Pacific region since its launch in 2002, returned to New Delhi, India after 12 years, with a conference attendance of 314 delegates. The 2018 conference had sessions on Big Data and Algorithms, Next Generation Sequencing and Omics Science, Structure, Function and Interactions, Disease and Drug Discovery and Plant and Agricultural Bioinformatics. The conference also featured an industry track as well as panel discussions on Women in Bioinformatics and Democratization vs. Quality control in academic publishing. Asia Pacific Bioinformatics Interaction & Networking Society (APbians) was launched as an APBionet Special Interest Group. Of the 52 oral presentations made, 22 were accepted in supplemental issues of BMC Bioinformatics, BMC Genomics or BMC Medical Genomics and are briefly reviewed here. Next year's InCoB will be held in Jakarta, Indonesia from September 10-12, 2019.

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Benchmarking of different molecular docking methods for protein-peptide docking

Cited by 108 publications

References 89 publications

Gene Expression Alterations and Molecular Analysis of CHEK1 in Solid Tumors

Gene Expression Alterations and Molecular Analysis of CHEK1 in Solid Tumors

Virtual Inhibition Analysis of Bioactive Compound Brazilin (Caesalpinia sappan L.) Toward Progesterone Receptor or Lonaprisan in Breast Cancer Proliferation

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

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