5b22493c29175b936b9e9ea11298e36a pmc_31261733.pdf b262b8580d74502728027ad9767d27d572984003 pmc_31261733.pdf eab0d66214dff2f0b136b44fe6d2ab5214cc443c6f452c374cd317762f75b502 pmc_31261733.pdf Title: 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns Subject: Discovering conserved three-dimensional (3D) patterns among protein structures may provide valuable insights into protein classification, functional annotations or the rational design of multi-target drugs. Thus, several computational tools have been developed to discover and compare protein 3D-patterns. However, most of them only consider previously known 3D-patterns such as orthosteric binding sites or structural motifs. This fact makes necessary the development of new methods for the identification of all possible 3D-patterns that exist in protein structures (allosteric sites, enzyme-cofactor interaction motifs, among others). In this work, we present 3D-PP, a new free access web server for the discovery and recognition all similar 3D amino acid patterns among a set of proteins structures (independent of their sequence similarity). This new tool does not require any previous structural knowledge about ligands, and all data are organized in a high-performance graph database. The input can be a text file with the PDB access codes or a zip file of PDB coordinates regardless of the origin of the structural data: X-ray crystallographic experiments or in silico homology modeling. The results are presented as lists of sequence patterns that can be further analyzed within the web page. We tested the accuracy and suitability of 3D-PP using two sets of proteins coming from the Protein Data Bank: (a) Zinc finger containing and (b) Serotonin target proteins. We also evaluated its usefulness for the discovering of new 3D-patterns, using a set of protein structures coming from in silico homology modeling methodologies, all of which are overexpressed in different types of cancer. Results indicate that 3D-PP is a reliable, flexible and friendly-user tool to identify conserved structural motifs, which could be relevant to improve the knowledge about protein function or classification. The web server can be freely utilized at ` `%%%`#`&12_`__~~~ Keywords: conserved patterns; similarity; 3D-patterns Author: Alejandro Valdés-Jiménez, Josep-L. Larriba-Pey, Gabriel Núñez-Vivanco and Miguel Reyes-Parada Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Fri Jun 28 12:59:09 2019 CEST ModDate: Fri Jun 28 12:59:09 2019 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 17 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 5633781 bytes Optimized: no PDF version: 1.5 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- GAVCUE+URWPalladioL-Ital Type 1 Custom yes yes no 89 0 EEHRBU+URWPalladioL-Bold Type 1 Custom yes yes no 90 0 NBMRRE+URWPalladioL-Roma Type 1 Custom yes yes no 91 0 CKUPDE+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 96 0 IRWHZX+TimesNewRomanPSMT Type 1C WinAnsi yes yes no 97 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 112 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 113 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 114 0 IYELBM+CMSY10 Type 1 Builtin yes yes no 253 0 CZKGAS+CMR10 Type 1 Builtin yes yes no 304 0 WEIJUK+CMSY9 Type 1 Builtin yes yes no 428 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2020-08-10 12:38:49 CEST RepresentationInformation: pmc_31261733.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2020-03-02 04:09:39 CET Size: 5633781 Format: PDF Version: 1.5 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 0 FreeObjects: 2 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: ぉのぴひはつふっぴどはの Item: Title: げづびふぬぴび Children: Item: Title: かのはぷのぜ〴ぜ〰こねちぬぬぜ〴ぜ〰〳い〭ぐちぴぴづひのび Children: Item: Title: ぐふぴちぴどぶづぜ〴ぜ〰ぎづぷぜ〴ぜ〰ずどのっぜ〴ぜ〰ぉはのぜ〴ぜ〰ぃははひつどのちぴどはのぜ〴ぜ〰こどぴづび Item: Title: ぐひはねどびっふはふびぜ〴ぜ〰あどのつどのでぜ〴ぜ〰こどぴづび Item: Title: ぎはぴぜ〴ぜ〰うはふのつぜ〴ぜ〰ぐちぴぴづひのび Item: Title: こづひはぴはのどのぜ〴ぜ〰ごちひでづぴぜ〴ぜ〰ぐひはぴづどのび Item: Title: うどのつどので〯いどびっはぶづひどのでぜ〴ぜ〰さのにのはぷのぜ〴ぜ〰〳い〭ぐちぴぴづひのびぜ〴ぜ〰はのぜ〴ぜ〰えはねはぬはでべぜ〴ぜ〰きはつづぬぜ〴ぜ〰こぴひふっぴふひづび Item: Title: ぃはねばちひどびはのぜ〴ぜ〰ぷどぴとぜ〴ぜ〰はぴとづひぜ〴ぜ〰きづぴとはつびぜ〴ぜ〰てはひぜ〴ぜ〰ぴとづぜ〴ぜ〰こづちひっとぜ〴ぜ〰ちのつぜ〴ぜ〰いづびっひどばぴどはのぜ〴ぜ〰はてぜ〴ぜ〰ぁねどのはぜ〴ぜ〰ぁっどつぜ〴ぜ〰ぐちぴぴづひのび Item: Title: きちぴづひどちぬびぜ〴ぜ〰ちのつぜ〴ぜ〰きづぴとはつび Children: Item: Title: ぇひどつぜ〴ぜ〰はてぜ〴ぜ〰ざどひぴふちぬぜ〴ぜ〰ぃははひつどのちぴづび Item: Title: ぐひはぴづどのぜ〴ぜ〰ぐひづばひはっづびびどので Item: Title: ぃひづちぴどはのぜ〴ぜ〰はてぜ〴ぜ〰ぴとづぜ〴ぜ〰ぇひちばとぜ〴ぜ〰いちぴちぢちびづび Item: Title: げづびふぬぴぜ〴ぜ〰ざどびふちぬどぺちぴどはの Item: Title: ぃはのっぬふびどはのび Item: Title: げづてづひづのっづび Filters: FilterPipeline: FlateDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 876 ImageHeight: 504 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/png ImageWidth: 679 ImageHeight: 530 ColorSpace: 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