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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | software resource, web application | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | 2026-08-29 11:24:51 | 6711 | |||||||
|
Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | data processing software, image analysis software, image reconstruction software, software application, software resource | A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab. | automation, molecular structure, xray crystallography, neutron crystallography, image reconstruction software |
is listed by: SoftCite is affiliated with: Phaser is related to: MolProbity has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA provides: Phenix.refine |
NIGMS | Available for download, Free for nonprofit work, Acknowledgement requested, For profit groups may access PHENIX through a Consortium agreement | https://www.phenix-online.org/documentation/ | SCR_014224 | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-08-29 11:24:46 | 11312 | |||||||
|
Duke University; North Carolina; USA Resource Report Resource Website 10+ mentions |
Duke University; North Carolina; USA (RRID:SCR_011193) | Duke | university | Private research university in Durham, North Carolina. Founded by Methodists and Quakers in 1838. Home of Blue Devils, Duke University has undergraduate and graduate students and world class faculty. | university, private, Durham, North Carolina |
uses: Benchling uses: Paperpile is related to: Clinical and Translational Science Awards Consortium is related to: Waxholm Space Atlas of the Sprague Dawley Rat Brain is related to: Coronavirus Immunotherapy Consortium is related to: Waxholm Space is parent organization of: EPIGEN is parent organization of: Purves Lab See For Yourself is parent organization of: Duke Model System Genomics is parent organization of: Diffusing Tensor Imaging in Java is parent organization of: PARalyzer is parent organization of: Center for In Vivo Microscopy is parent organization of: Drug-Induced Liver Injury Network is parent organization of: Duke University of North Carolina Brain Imaging and Analysis Center Core Facility is parent organization of: CAMRD is parent organization of: Duke University Medical Center: Duke Image Analysis Laboratory is parent organization of: NASTIseq is parent organization of: OSA is parent organization of: CIGAL is parent organization of: Addiction Research GPCR Assay Bank is parent organization of: BioPerl is parent organization of: CERAD - Consortium to Establish a Registry for Alzheimer's Disease is parent organization of: Duke University, Pharmacology and Cancer Biology is parent organization of: Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience is parent organization of: Duke Biobank is parent organization of: Duke Biospecimen Repository is parent organization of: NESCent - National Evolutionary Synthesis Center is parent organization of: Adult Wistar Rat Atlas is parent organization of: Duke University Medical Center Neuropsychiatric Imaging Research Laboratory is parent organization of: Duke University NeuroAnatomy Web Resources is parent organization of: High Quality SNP Database is parent organization of: Avian Brain is parent organization of: T-One weighted Perfusion imaging Parameter CAlculation Toolkit is parent organization of: 3D Macromolecular Analysis and Kinemage Home Page is parent organization of: Tropical Disease Initiative is parent organization of: National Long Term Care Survey is parent organization of: MicroMUMMIE is parent organization of: Duke University School of Medicine; North Carolina; USA is parent organization of: Duke IGSP Genome Sequencing and Analysis Core is parent organization of: Duke University Labs and Facilities is parent organization of: Duke Neurotransgenic Laboratory is parent organization of: Duke DNA Microarray Core Facility is parent organization of: Duke Clinical Research Unit is parent organization of: Biospecimen Repository and Processing Core is parent organization of: Duke Human Heart Repository is parent organization of: Chinese Longitudinal Healthy Longevity Survey (CLHLS) is parent organization of: Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) is parent organization of: MolProbity is parent organization of: Cvapp is parent organization of: Duke O'Brien Center for Kidney Research Clinical and Translational Core is parent organization of: Duke O'Brien Center for Kidney Research Renal Genomics Core is parent organization of: Duke O'Brien Center for Kidney Research is parent organization of: Duke O'Brien Center for Kidney Research Animal Models Core is parent organization of: Duke University Omics Data Analysis Core Facility is parent organization of: Pediatric Obesity Microbiome and Metabolism Study is parent organization of: Duke University Shared Materials Instrumentation Facility (SMIF) is parent organization of: Duke University Light Microscopy Core Facility |
, ISNI 0000 0004 1936 796, GRID grid.26009.3d, Crossref Funder ID 100006510, nif-0000-1934, Wikidata Q168751 | https://ror.org/00py81415 | SCR_011193 | Duke University | 2026-08-29 11:23:53 | 14 | |||||||
|
Coot Resource Report Resource Website 10000+ mentions |
Coot (RRID:SCR_014222) | COOT | data or information resource, model, simulation software, software application, software resource, software toolkit | Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available. | software toolkit, simulation software, model manipulation, protein modeling, bio.tools |
is used by: PDB-REDO is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MolProbity has parent organization: MRC Laboratory of Molecular Biology |
PMID:15572765 | Available for download, Acknowledgement requested | biotools:coot | http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot, https://bio.tools/coot | SCR_014222 | Crystallographic Object-Oriented Toolkit | 2026-08-29 11:24:43 | 15682 | |||||
|
SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | data or information resource, knowledge base, portal, project portal, software resource | Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. | Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, |
lists: ProteinPilot lists: ROCit lists: survivalROC lists: GIFT lists: PyWavelets lists: pRRophetic lists: GOplot lists: Rgdal lists: riskRegression lists: RNAfold lists: RNALocate lists: pyPCcazip lists: ScanProsite lists: RapGreen lists: ABySS lists: AMBER lists: ANNOVAR lists: ASAP lists: ASPicDB lists: AStalavista lists: ATSAS lists: Alien hunter lists: Adobe Photoshop lists: Affymetrix lists: Augustus lists: Argus lists: Adobe Illustrator lists: ART lists: AutoDock Vina lists: AutoDock lists: ANALYZE lists: BLASTClust lists: arrayQualityMetrics lists: BLASTN lists: BLASTX lists: BLASTP lists: Bowtie lists: Autogrid lists: BRB-ArrayTools lists: BEDTools lists: BWA lists: BioEdit lists: BRASS lists: Bioconductor lists: BioExtract lists: BaCelLo lists: BioMoby lists: Brain Extraction Tool lists: Bowtie 2 lists: BoxPlotR lists: biomaRt lists: BioPerl lists: CANGS lists: CFX Manager lists: CEAS lists: BlobFinder lists: CLC Genomics Workbench lists: BREAKDANCER lists: CASAVA lists: CLC Main Workbench lists: ClustalW lists: Clustal W2 lists: ComBat lists: CCP4 lists: Blender lists: Coot lists: CGView lists: COMSOL Multiphysics lists: CTFFIND lists: CalcuSyn lists: ChIPpeakAnno lists: Chimera lists: CVODE lists: DAVID lists: Cufflinks lists: caret lists: ClueGO lists: Cluster lists: Clocklab lists: DIANA-mirPath lists: Cytoscape lists: EMAN lists: E-Prime lists: DESeq2 lists: Definiens Developer XD lists: Eigensoft lists: EMBOSS lists: Ensembl lists: DIALIGN lists: Design-Expert lists: EndNote lists: CMAP lists: EEGLAB lists: CMap lists: Epi Info lists: FASTA lists: Ensembl Genome Browser lists: Epik lists: FACS lists: FCS Express lists: Flowlogic lists: FSL lists: FLASH lists: FATCAT lists: FastQC lists: G*Power lists: GOLD lists: FGENESH lists: FreeSurfer lists: FlowJo lists: GeneTools lists: Galaxy lists: GATK lists: ELDA lists: GraphPad lists: GRADEpro lists: Fiji lists: Gblocks lists: FigTree lists: GENIE lists: GBrowse lists: Gemma lists: GeneChip Operating Software lists: GeneMapper lists: GeneMarker lists: GenABEL lists: GenePattern lists: GraphPad Prism lists: GenePix Pro lists: Google lists: Genesis lists: Hologic lists: GeneSpring GX lists: GeneVenn lists: HaploReg lists: Google Scholar lists: HALO lists: Gwyddion lists: IMAGIC lists: HKL-2000 lists: Glide lists: Glimmer lists: I-TASSER lists: GenomeStudio lists: IMOD lists: Haploview lists: Hmmer lists: Hydra lists: IUPRED lists: HomeCageScan lists: Geneious lists: IGOR Pro lists: IMPUTE lists: Infernal lists: Image-Pro Plus lists: JASP lists: LSM Image Examiner lists: Imaris lists: Image Pro Plus lists: ImageQuant lists: ImageJ lists: Integrative Genomics Viewer lists: jcvi lists: InterProScan lists: KaleidaGraph lists: Ligprep lists: Heidelberg Eye Explorer lists: JMP lists: Ingenuity Pathways Knowledge Base lists: Leica QWin lists: JCB DataViewer lists: Jalview lists: LigandScout lists: Ingenuity Pathway Analysis lists: LabView lists: Kepler lists: MAFFT lists: Jmol lists: ImageScope lists: MACS lists: Maq lists: MUMmer lists: MATLAB lists: Mimics lists: MACH lists: MCODE lists: Mascot lists: Maestro lists: MSQuant lists: MediaWiki lists: MINC lists: MRIcron lists: MOE lists: ModFit LT lists: LIMMA lists: MassLynx lists: mitopred lists: MrBayes lists: MolProbity lists: MUSCLE lists: MutationAssessor lists: MaxQuant lists: Minitab lists: MODELLER lists: MetaboAnalyst lists: MedCalc lists: Origin lists: MPlus lists: MutationTaster lists: MuTect lists: Multi Gauge lists: NIA Array Analysis lists: NIH Image lists: Phenix lists: MycoBank lists: OpenClinica lists: Nexus lists: OMTools lists: NIS-Elements lists: PAST lists: NVivo lists: PRISM (Stanford database) lists: Metscape lists: PROCHECK lists: oligo lists: OpenEpi lists: Pathway Commons lists: Nanoparticle Tracking Analysis lists: Openlab lists: PLINK lists: PAUP lists: NONMEM lists: PREFAB lists: NetworkX lists: PeptideProphet lists: Primer Designer lists: PhyML lists: PASS lists: PyMOL lists: PSIPRED lists: PROFILER lists: PHYLIP lists: Phobius lists: Prime lists: Phyutility lists: Picard lists: ProteinProphet lists: Phaser lists: ProSAS lists: PostgreSQL lists: Primer-BLAST lists: ProteinLynx Global Server lists: QUANTO lists: Primer Express lists: Primer3Plus lists: ProtTest lists: ProbCons lists: Primer3 lists: Poretools lists: Protein preparation Wizard lists: QmRLFS-finder lists: PicTar lists: RevMan lists: Pipeline Pilot lists: QIIME lists: PRISMA lists: REDCap lists: RAxML lists: Proteome Discoverer lists: Research Randomizer lists: SPARTAN lists: SPSS lists: RNAstructure lists: Refmac lists: QuantPrime lists: Prodigal lists: RepeatModeler lists: Ringo lists: SQLite lists: SAGE lists: Rhinoceros lists: SAMTOOLS lists: SPAdes lists: RepeatMasker lists: SEDFIT lists: STATISTICA lists: RNAhybrid lists: SlideBook lists: STRUCTURE lists: SABmark lists: SPM lists: Stata lists: RStudio lists: SciPy lists: Scion Image lists: Simulink lists: TAGGER lists: TopHat lists: SAM lists: ShortRead lists: SIFT lists: SCAN lists: SignalP lists: Scopus lists: Strelka2 lists: Trans-ABySS lists: Statgraphics Centurion lists: T-Coffee lists: Statistical Analysis System lists: TargetScan lists: UCHIME lists: Sequencher lists: SigmaStat lists: UCSC Genome Browser lists: affy lists: Taverna lists: MBF BioScience: Stereo Investigator lists: Trimmomatic lists: Vmatch lists: WFU PickAtlas lists: SigmaPlot lists: X!Tandem lists: STAR lists: TASSEL lists: SyStat lists: WEBLOGO lists: UCSF Chimera lists: TreeView lists: pheatmap lists: WinWCP lists: microRNA.org lists: glmnet lists: Phenix.refine lists: BASE lists: beadarray lists: RMS lists: lumi lists: Web of Science lists: minfi lists: geNORM lists: WU-BLAST lists: WinBUGS lists: SPP lists: tRNAscan-SE lists: WebPlotDigitizer lists: qBasePLUS lists: Matplotlib lists: TreeBASE lists: pClamp lists: TBLASTN lists: igraph lists: V3D lists: survival lists: miRanda lists: piRNABank lists: topGO lists: NGmerge lists: OMNISEC lists: NOTUNG lists: OpenBUGS lists: Optimization Toolbox lists: ProgRes Capture Pro lists: Ocular lists: Umediation lists: Nano Measurer lists: PHYLDOG lists: VSEARCH lists: WinNonlin lists: WHONET lists: ToposPro lists: Treerecs lists: Agilent Seahorse Wave lists: SimPhy lists: TomoStudio lists: Mutation Assessor lists: Stem lists: SRAMP lists: CRISPResso2 lists: geepack lists: Evalue lists: DAGitty lists: FastMulRFS lists: ggridges lists: gamm4 lists: AutoRT lists: CopyKAT lists: Inference of CRISPR Edits lists: classInt lists: ASTRAL-Pro lists: maftools lists: mitml lists: CMplot lists: MetaPSICOV lists: LaCyTools lists: MADOKA lists: Kaplan Meier Plotter lists: IntFOLD lists: ModFOLD lists: lDDT has parent organization: University of Texas at Austin; Texas; USA |
Sloan Foundation | DOI:10.1002/asi.24454 | Free, Available for download, Freely available | https://github.com/softcite/softcite_dataset_v2, https://zenodo.org/record/7995565 | SCR_024411 | Software Citation | 2026-08-29 11:28:10 | 0 |
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