Tools   Select Another Resource Report Type

http://www.ebi.ac.uk/thornton-srv/databases/CSA/

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme. The CSA contains 2 types of entry: 1. Original hand-annotated entries, derived from the primary literature. References for these entries are given. 2. Homologous entries, found by PSI-BLAST alignment (using an e value cut-off of 0.00005) to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented. Access to the CSA is via PDB code, SWISS-PROT entry or E.C. number. Accessing via PDB code takes you straight to the CSA entry for that PDB, while accessing via SWISS-PROT or E.C. number gives a list of all PDB codes for structures assigned that particular SWISS-PROT identifier or E.C. number. Structures with entries in the CSA are given as hyperlinks. Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either Literature reference or PSI-BLAST hit. If the entry is a PSI-BLAST hit you can follow the link to the original entry. You may download the CSA. JESS, an algorithm for constraint-based structural template matching and its application to 3D templates used by the CSA, is available for download.

Proper citation: CSA - Catalytic Site Atlas (RRID:SCR_013099) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/ligmap/files/

A tool for structural biology and drug design.

Proper citation: AutoMap (RRID:SCR_013095) Copy   

•   Source: SciCrunch Registry
  

http://www.csrees.usda.gov/

Proper citation: USDA National Institute of Food and Agriculture (RRID:SCR_012886) Copy   

•   Source: SciCrunch Registry
  

http://www.nigms.nih.gov/

NIGMS supports basic biomedical research that is not targeted to specific diseases. NIGMS funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells, how our bodies use energy, and how we respond to medicines. The results of this research increase our understanding of life and lay the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS also supports research training programs that produce the next generation of biomedical scientists, and it has special programs to encourage underrepresented minorities to pursue biomedical research careers. The National Institute of General Medical Sciences (NIGMS) primarily supports research that lays the foundation for advances in disease diagnosis, treatment, and prevention. The Institute's research training programs help provide the next generation of scientists. Each year, NIGMS-supported scientists make many advances in understanding fundamental life processes. In the course of answering basic research questions, these investigators increase our knowledge about the mechanisms and pathways involved in certain diseases. Institute grantees also develop important new tools and techniques, some of which have medical applications. In recognition of the significance of their work, a number of NIGMS grantees have received the Nobel Prize and other high scientific honors. At any given time, NIGMS supports approximately 4,700 research grants—approximately 11 percent of the grants funded by NIH as a whole. NIGMS also supports approximately 26 percent of the trainees who receive assistance from NIH. NIGMS also supports approximately 25% of the trainees who receive assistance from NIH. The Institute places great emphasis on supporting investigator-initiated research grants. It funds a limited number of research center grants in selected fields, including structural genomics, trauma and burn research, and systems biology. In addition, NIGMS supports several important scientific resources, including the NIGMS Human Genetic Cell Repository and the Protein Data Bank.

Proper citation: National Institute of General Medical Sciences (RRID:SCR_012887) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry
  

https://www.niddk.nih.gov/

Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.

Proper citation: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BRAINSia/BRAINSTools

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme.

Proper citation: BRAINSTracer (RRID:SCR_012894) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry
  

http://derisilab.ucsf.edu/software/price/index.html

Software for a de novo genome assembler implemented in C++.

Proper citation: PRICE (RRID:SCR_013063) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar

Accurate error-correction of amplicon pyrosequences.

Proper citation: Acacia (RRID:SCR_012896) Copy   

•   Source: SciCrunch Registry
  

http://www.nhlbi.nih.gov/about/dld/

Supports research on the causes, diagnosis, prevention, and treatment of lung diseases and sleep disorders. Research is funded through investigator-initiated and Institute-initiated grant programs and through contract programs in areas including asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease, cystic fibrosis, respiratory neurobiology, sleep-disordered breathing, critical care and acute lung injury, developmental biology and pediatric pulmonary diseases, immunologic and fibrotic pulmonary disease, rare lung disorders, pulmonary vascular disease, and pulmonary complications of AIDS and tuberculosis. The Division is responsible for monitoring the latest research developments in the extramural scientific community as well as identifying research gaps and needs, obtaining advice from experts in the field, and implementing programs to address new opportunities. The DLD has three branches, the Airway Biology and Disease Branch, the Lung Biology and Disease Branch, and the National Center on Sleep Disorders Research.

Proper citation: NHLBI Division of Lung Diseases (RRID:SCR_013074) Copy   

•   Source: SciCrunch Registry
  

http://www.ssa.gov/

Independent agency of the U.S. federal government that administers Social Security, a social insurance program consisting of retirement, disability, and survivor benefits.

Proper citation: U.S. Social Security Administration (RRID:SCR_012905) Copy   

•   Source: SciCrunch Registry
  

http://www.aasld.org/Pages/Default.aspx

A non-profit organization of scientists and healthcare professionals committed to preventing and curing liver disease, which runs three journals and an annual meeting. Its mission is to Advance the Science and Practice of Hepatology, Liver Transplantation and Hepatobiliary Surgery, Thereby Promoting Liver Health and Optimal Care of Patients with Liver and Biliary Tract Diseases. AASLD was founded in 1950 by a small group of leading liver specialists (including Hans Popper, Leon Schiff, Fred Hoffbauer, Cecil Watson, Jesse Bollman, and Sheila Sherlock, to name a few) to bring together those who had contributed to the field of hepatology. AASLD has grown to an international society responsible for all aspects of hepatology, and our annual meeting, The Liver Meeting, has grown in attendance from 12 to over 7,000 physicians, surgeons, researchers, and allied health professionals from around the world. AASLD sponsors two to four Single Topic Conferences each year in clinical, basic, hepatitis, or pediatric hepatology. Our two monthly journals, HEPATOLOGY and Liver Transplantation, provide the latest research findings for hepatology and surgery of the liver. AASLD''s membership includes ALL professionals dedicated to hepatobiliary discoveries and patient care. Mentoring, the sharing of knowledge, and dedication to professional growth and development are among the core values of AASLD and its members.

Proper citation: AASLD - American Association for the Study of Liver Diseases (RRID:SCR_012900) Copy   

•   Source: SciCrunch Registry
  

http://www2.hu-berlin.de/eyetracking-eeg

A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line.

Proper citation: EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) Copy   

•   Source: SciCrunch Registry
  

http://genome.dkfz-heidelberg.de/cgi-bin/GENSCAN/genscan.cgi

Resource out of service. Documented on February 24,2021.

Proper citation: GENSCAN (RRID:SCR_012902) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/help/mailing-list/

This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor.

Proper citation: Bioconductor mailing list (RRID:SCR_012915) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/assembly

Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).

Proper citation: NCBI Assembly Archive Viewer (RRID:SCR_012917) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.wehi.edu.au/featureCounts/

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

Proper citation: featureCounts (RRID:SCR_012919) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry