Tools   Select Another Resource Report Type

https://www.datanator.info

Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.

Proper citation: Datanator (RRID:SCR_018651) Copy   

•   Source: SciCrunch Registry
  

http://pic.mbu.iisc.ernet.in

Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex.

Proper citation: Protein Interactions Calculator (RRID:SCR_018574) Copy   

•   Source: SciCrunch Registry
  

http://lrpath.ncibi.org/

Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.

Proper citation: LRPath (RRID:SCR_018572) Copy   

•   Source: SciCrunch Registry
  

https://www.machado.cnptia.embrapa.br/plantannot

Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard.

Proper citation: Plant Co-expression Annotation Resource (RRID:SCR_018429) Copy   

•   Source: SciCrunch Registry
  

http://galaxy.seoklab.org/

Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined.

Proper citation: GalaxyWEB (RRID:SCR_018558) Copy   

•   Source: SciCrunch Registry
  

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

Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area.

Proper citation: MaxAlign (RRID:SCR_018552) Copy   

•   Source: SciCrunch Registry
  

http://huanglab.phys.hust.edu.cn/hpepdock/

Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.

Proper citation: HPEPDOCK Server (RRID:SCR_018561) Copy   

•   Source: SciCrunch Registry
  

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry
  

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SouthGreenPlatform/metaXplor

Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.

Proper citation: metaXplor (RRID:SCR_019025) Copy   

•   Source: SciCrunch Registry
  

https://github.com/LCSB-BioCore/GigaSOM.jl

Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.

Proper citation: GigaSOM.jl (RRID:SCR_019020) Copy   

•   Source: SciCrunch Registry
  

https://github.com/acg-team/tral

Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

Proper citation: TRAL (RRID:SCR_018979) Copy   

•   Source: SciCrunch Registry
  

http://www.prognoscan.org/

Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets.

Proper citation: PrognoScan (RRID:SCR_018740) Copy   

•   Source: SciCrunch Registry
  

https://evcouplings.org/

Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.

Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) Copy   

•   Source: SciCrunch Registry
  

http://crdd.osdd.net/raghava/vicmpred/index.html

Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.

Proper citation: VICMpred (RRID:SCR_019039) Copy   

•   Source: SciCrunch Registry
  

http://annotree.uwaterloo.ca/

Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.

Proper citation: Annotree (RRID:SCR_018980) Copy   

•   Source: SciCrunch Registry
  

http://pyntacle.css-mendel.it/

Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools.

Proper citation: Pyntacle (RRID:SCR_019030) Copy   

•   Source: SciCrunch Registry
  

http://www.imgt.org/StatClonotype/

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy   

•   Source: SciCrunch Registry
  

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) Copy   

•   Source: SciCrunch Registry
  

https://github.com/HicServices/DicomTypeTranslation

Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database.

Proper citation: DicomTypeTranslator (RRID:SCR_018878) Copy   

•   Source: SciCrunch Registry