Tools   Select Another Resource Report Type

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Web tool for conserved domains searching within protein or coding nucleotide sequence.

Proper citation: Conserved Domains Search (RRID:SCR_018729) Copy   

•   Source: SciCrunch Registry

http://pinet-server.org

Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

Proper citation: piNET (RRID:SCR_018693) Copy   

•   Source: SciCrunch Registry

https://robetta.bakerlab.org/

Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure.

Proper citation: Robetta (RRID:SCR_018805) Copy   

•   Source: SciCrunch Registry

http://protein.ict.ac.cn/FALCON/

Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction.

Proper citation: FALCON (RRID:SCR_018804) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/DiscoTope/

Web server to predict discontinuous B cell epitopes from protein three dimensional structures.

Proper citation: DiscoTope (RRID:SCR_018530) Copy   

•   Source: SciCrunch Registry

https://prosa.services.came.sbg.ac.at/prosa.php

Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.

Proper citation: ProSA-web (RRID:SCR_018540) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) Copy   

•   Source: SciCrunch Registry

http://www.conplot.org/

Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.

Proper citation: ConPlot (RRID:SCR_019216) Copy   

•   Source: SciCrunch Registry

https://github.com/Sung-Huan/ANNOgesic

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

Proper citation: ANNOgesic (RRID:SCR_016326) Copy   

•   Source: SciCrunch Registry

http://cajadb.neuro.ufrn.br

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

Proper citation: CajaDB (RRID:SCR_016506) Copy   

•   Source: SciCrunch Registry

https://www.genome.jp/tools/dinies/

Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.

Proper citation: DINIES (RRID:SCR_016505) Copy   

•   Source: SciCrunch Registry

http://www.compbio.dundee.ac.uk/jpred/

Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.

Proper citation: Jpred (RRID:SCR_016504) Copy   

•   Source: SciCrunch Registry

http://bioinf.bio.uth.gr/nat-ncs2

Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.

Proper citation: NAT/NCS2 Hound (RRID:SCR_016473) Copy   

•   Source: SciCrunch Registry

https://imaps.genialis.com/iclip

Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.

Proper citation: iMaps (RRID:SCR_016705) Copy   

•   Source: SciCrunch Registry

https://github.com/tomazc/iCount

Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.

Proper citation: iCount (RRID:SCR_016712) Copy   

•   Source: SciCrunch Registry

http://projects.biotec.tu-dresden.de/metapocket/

Software tool to identify pockets on protein surface to predict ligand-binding sites.

Proper citation: metaPocket (RRID:SCR_016653) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/orffinder

Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.

Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy   

•   Source: SciCrunch Registry