2021
DOI: 10.1155/2021/2327832
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Prediction of Metal Ion Binding Sites of Transmembrane Proteins

Abstract: The metal ion binding of transmembrane proteins (TMPs) plays a fundamental role in biological processes, pharmaceutics, and medicine, but it is hard to extract enough TMP structures in experimental techniques to discover their binding mechanism comprehensively. To predict the metal ion binding sites for TMPs on a large scale, we present a simple and effective two-stage prediction method TMP-MIBS, to identify the corresponding binding residues using TMP sequences. At present, there is no specific research on th… Show more

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Cited by 6 publications
(4 citation statements)
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“…An impressive number of methods were proposed, such as MEMSAT [81,82], HTP [83], DAS [83], SOSUI [84], HMMTOP [85,86], TMHMM 1.0 [87], PRED-TMR [88], OCTOPUS [89], TOPCONS [90,91], MINNOU [92], SVMtm [93], TUPS [94], Localizome [95], MemBrain [96], AllesTM [97], TMPSS [98], and TMbed [99]. The most recent approaches also take into account other features, such as the regions of the protein that actually face the membrane, the cytosolic or extracellular sides, and the motifs responsible for the interactions [97,[100][101][102].…”
Section: Discussionmentioning
confidence: 99%
“…An impressive number of methods were proposed, such as MEMSAT [81,82], HTP [83], DAS [83], SOSUI [84], HMMTOP [85,86], TMHMM 1.0 [87], PRED-TMR [88], OCTOPUS [89], TOPCONS [90,91], MINNOU [92], SVMtm [93], TUPS [94], Localizome [95], MemBrain [96], AllesTM [97], TMPSS [98], and TMbed [99]. The most recent approaches also take into account other features, such as the regions of the protein that actually face the membrane, the cytosolic or extracellular sides, and the motifs responsible for the interactions [97,[100][101][102].…”
Section: Discussionmentioning
confidence: 99%
“…(2) Evolutionary Profile-Based Features . Recent studies [ 54 , 56 , 57 , 80 , 81 ] pointed out that functional or structural important residues tend to show higher evolutionary conservation. The conserved residues are usually involved in enzyme activity, ligand binding, or protein structural stability [ 82 ].…”
Section: Methods Development Of Metal-binding Predictionmentioning
confidence: 99%
“…Three methods, namely, znMachine [ 51 ], ZincBinder [ 103 ], and FunFOLD [ 155 ], provide both web server and standalone software. TMP_MIBS [ 54 ] is designed to predict general metal-binding residues and deployed using the Python language. DELIA [ 80 ] requires PDB-formatted 3D coordinates input and produces both binary prediction and putative probability of a residue being potential specific metal-binding.…”
Section: Methods Development Of Metal-binding Predictionmentioning
confidence: 99%
“…The interactive network is demonstrated by Cytoscape software. Using RoseTTAFold (https://robetta.bakerlab.org accessed on 13 November 2022) and MIB database (http: //bioinfo.cmu.edu.tw/MIB/, accessed on 13 November 2022), the six StSROs protein crystal structures were analyzed [60,61], then PyMOL plugin was used to refine and analyze the predicted protein tertiary structure.…”
Section: Stsro Family Interaction Network Analysis and Proteins Terti...mentioning
confidence: 99%