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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | image analysis software, image reconstruction software, software application, software resource, data processing software | 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 | 2026-07-31 09:27:26 | 10587 | |||||||
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Lawrence Berkeley National Laboratory Resource Report Resource Website 1+ mentions |
Lawrence Berkeley National Laboratory (RRID:SCR_011336) | institution | Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2010 is $707 million, with an additional $104 million in funding from the American Recovery and Reinvestment Act, for a total of $811 million. |
is listed by: DataCite is related to: 1000 Fungal Genome Project has parent organization: University of California; California; USA is parent organization of: National Center for X-ray Tomography is parent organization of: Alignable Tight Genomic Cluster is parent organization of: RegPrecise is parent organization of: Assembly/Alignment/Annotation of 12 Related Drosophila Species is parent organization of: BioPig is parent organization of: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation is parent organization of: MicrobesOnline is parent organization of: Berkeley Bioinformatics Open-Source Projects is parent organization of: Alternative Splicing Database is parent organization of: MeRNA is parent organization of: VISTA Enhancer Browser is parent organization of: Phenote: A Phenotype Annotation Tool using Ontologies is parent organization of: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis is parent organization of: Berkeley Drosophila Transcription Network Project is parent organization of: VISTA Browser is parent organization of: Greengenes is parent organization of: go-moose is parent organization of: Phytozome is parent organization of: Phenix is parent organization of: University of California at Berkeley National Energy Research Scientific Computing Core Facility |
Crossref funder ID: 100006235, Wikidata: Q1133630, nlx_37075, grid.184769.5, ISNI: 0000 0001 2231 4551 | https://ror.org/02jbv0t02, https://api.datacite.org/dois?prefix=10.7941 | SCR_011336 | Berkeley Lab, Lawrence Berkeley National Lab | 2026-07-25 12:07:16 | 4 | |||||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | software resource, software application, data processing software | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-07-30 09:30:03 | 39 | ||||||
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University of California at Berkeley; Berkeley; USA Resource Report Resource Website 1+ mentions |
University of California at Berkeley; Berkeley; USA (RRID:SCR_011618) | university | Public research university in the United States. Located in the city of Berkeley, it was founded in 1868 and serves as the flagship institution of the ten research universities affiliated with the University of California system. Berkeley ranks 5th internationally in the Academic Ranking of World Universities. |
uses: Benchling uses: Paperpile uses: GenomeCompiler is related to: The Pancreatic Beta-Cell Consortium is related to: BBmap is related to: FastProject is related to: University of California at Berkeley National Energy Research Scientific Computing Core Facility has parent organization: University of California; California; USA is parent organization of: brainSCANr is parent organization of: AmphibiaWeb is parent organization of: IPython is parent organization of: ASTRAL Compendium for Sequence and Structure Analysis is parent organization of: Helen Wills Neuroscience Institute is parent organization of: Human Mortality Database is parent organization of: OBD-PKB Interface is parent organization of: ORNIS is parent organization of: BioText Search Engine is parent organization of: SPH Biorepository is parent organization of: SLIDE is parent organization of: Werblin Lab is parent organization of: SysCall is parent organization of: Scalable Nucleotide Alignment Program is parent organization of: CRCNS is parent organization of: eXpress is parent organization of: MetMap is parent organization of: PhyloFacts is parent organization of: Spatio- Spectro- Temporal Receptive Field is parent organization of: Mammal Networked Information System is parent organization of: Flow Cytometers Facility is parent organization of: WEBLOGO is parent organization of: WorldClim is parent organization of: Museum of Vertebrate Zoology is parent organization of: UC Berkeley Marvell Nanofabrication Laboratory is parent organization of: UC Berkeley Molecular Imaging Center Core Facility is parent organization of: UC Berkeley Brain Imaging Center is parent organization of: University of California Berkeley Labs and Facilities is parent organization of: Berkeley Drosophila Genome Project is parent organization of: FishNet2 is parent organization of: TreeView is parent organization of: Cluster is parent organization of: ScanAlyze is parent organization of: EISEN LAB is parent organization of: timecourse is parent organization of: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation is parent organization of: Neuroimaging in Python is parent organization of: Phenix is parent organization of: PAML is parent organization of: Neurodata Without Borders is parent organization of: BOINC - Berkeley Open Infrastructure for Network Computing is parent organization of: AMAP is parent organization of: FSA is parent organization of: Apache Spark is parent organization of: TopHat is parent organization of: Shannon is parent organization of: Fitness Browser is parent organization of: PostgreSQL is parent organization of: Feldman Lab Lickometer project is parent organization of: DIY Rodent Running Disk is parent organization of: StrVCTVRE is parent organization of: University of California at Berkeley QB3 Genomics Core Facility is parent organization of: University of California at Berkeley QB3 High Throughput Screening CoreFacility is parent organization of: CORAL is parent organization of: University of California Berkeley QB3 Cell and Tissue Analysis Core Facility is parent organization of: University of California at Berkeley Electron Microscope Laboratory Core Facility is parent organization of: Berkeley Seismological Laboratory is parent organization of: University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility is parent organization of: University of California at Berkeley Cal-Cryo QB3-Berkeley Core Facility |
, GRID: grid.47840.3f, Wikidata Q168756, ISNI: 0000 0001 2181 7878, Crossref Funder: ID 100006978, nlx_94506 | https://ror.org/01an7q238 | SCR_011618 | , Berkeley, University of California, UCBerkeley, University of California; Berkeley; USA, UC Berkeley, University of California at Berkeley; USA | 2026-07-25 12:13:50 | 5 | |||||||||
|
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 | 2026-07-30 09:29:13 | 6313 | |||||||
|
Phaser Resource Report Resource Website 1000+ mentions |
Phaser (RRID:SCR_014219) | image analysis software, image reconstruction software, data acquisition software, software application, software resource, data processing software | Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods. | crystallographic software, molecular replacement, experimental phasing method, data acquisition software, image analysis software, image reconstruction software |
is listed by: SoftCite is affiliated with: Phenix has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:19461840 | Available through Phenix, Available through CCP4, Acknowledgement requested | http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software | SCR_014219 | 2026-07-31 09:27:26 | 2572 | ||||||||
|
SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | project portal, data or information resource, portal, knowledge base, 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 | 2026-07-31 09:29:25 | 0 |
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