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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
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
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
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
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
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
Software tool for efficiently solving large scale sequence matching tasks.
Proper citation: Vmatch (RRID:SCR_018968) Copy
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
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
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
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
https://github.com/BackofenLab/StoatyDive
Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.
Proper citation: StoatyDive (RRID:SCR_018796) Copy
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
https://github.com/auranic/ClinTrajan
Software Python package for analysis of trajectories in clinical datasets.
Proper citation: ClinTrajAn (RRID:SCR_019018) Copy
Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.
Proper citation: Seqtk (RRID:SCR_018927) Copy
https://github.com/sandmanns/CopyDetective
Software tool for detection threshold aware CNV calling in matched whole exome sequencing data.
Proper citation: CopyDetective (RRID:SCR_018909) Copy
https://github.com/cochran4/GEMB
Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.
Proper citation: GEMB (RRID:SCR_018904) Copy
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
https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.
Proper citation: Batch Web CD-Search Tool (RRID:SCR_018756) Copy
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Proper citation: RiboTaper (RRID:SCR_018880) Copy
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