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http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.

Proper citation: DichroWeb (RRID:SCR_018125) Copy   

•   Source: SciCrunch Registry
  

https://github.com/gevaertlab/BetaVAEImputation

Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis.

Proper citation: betaVAEImputation (RRID:SCR_018730) Copy   

•   Source: SciCrunch Registry
  

http://crispr-era.stanford.edu/index.jsp

Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.

Proper citation: CRISPR-ERA (RRID:SCR_018710) Copy   

•   Source: SciCrunch Registry
  

https://milaboratory.com/software/mixcr/

Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling.

Proper citation: MiXCR (RRID:SCR_018725) Copy   

•   Source: SciCrunch Registry
  

https://www.bcforms.org

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

Proper citation: BcForms (RRID:SCR_018654) Copy   

•   Source: SciCrunch Registry
  

http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE

Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.

Proper citation: GalaxyRefine (RRID:SCR_018531) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/EpiEstim/index.html

Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series.

Proper citation: EpiEstim (RRID:SCR_018538) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=precrec

Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.

Proper citation: precrec (RRID:SCR_018659) Copy   

•   Source: SciCrunch Registry
  

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