Curator Dashboard

EnzyMiner automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability or the activity of a given enzyme. For querying EnzyMiner, please choose an enzyme from the list and specify if you are interested in disease related abstracts or non-disease related abstracts. For disease related abstracts, the mutation list and direct links to the abstracts will be displayed. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme''s stability or functionality. If your target enzyme is not in the list, please write the enzyme name to the query box. We will run the EnzyMiner for the desired enzyme and add the results to our database. EnzyMiner has been developed by Computational Biology Lab of Sabanci University.

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• SciCrunch
• 16 years ago - by Anonymous

Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization.

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• SciCrunch
• 12 years ago - by Anonymous

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

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• SciCrunch
• 14 years ago - by Anonymous

An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.

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• SciCrunch
• 13 years ago - by Anonymous

A blog by Zen Faulkes, an invertebrate neuroethologist at The University of Texas-Pan American.

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• SciCrunch
• 14 years ago - by Anonymous

A blog about neuromarketing, a research methodology born of the fusion of neuroscience and research techniques of conventional marketing in Spanish by Sergio Monge. If you want to read it in English, Google translate does a good job. A good way to learn about practical applications of neuroscience to a field with little exposure in conventional neuroscience academia. The neuromarketing is a branch of market research that uses biometric measurement systems in their studies (EEG, MRI, galvanic skin response, eye-tracking, heart rate ...). One of the most significant differences with conventional research neuromarketing is not content with the verbal statements of the subjects, but aims to go further, unraveling the effect of the unconscious and emotions in decision-making. The author of Neuromarca is Sergio Monge, Degree in Advertising and Public Relations and PhD in Audiovisual Communication and Advertising from the University of the Basque Country / Euskal Herriko Universitatea. Sergio has experience in the field of Corporate Communications and is familiar with the blogosphere and the Internet communication environment. He currently teaches full time for the UPV / EHU and offers some services such as communications and marketing consultant. The interest of the author of this blog by neuroscience and neuromarketing longstanding but his attendance Neuro Connections conference, held from 5 to 7 febreo 2009 in Krakow (Poland), is the main reason he began writing Neuromarca. The intention is that Neuromarca is a repository of articles in Spanish about neuromarketing, so that could be a reference to the Hispanic blogosphere in this emerging discipline.

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• SciCrunch
• 14 years ago - by Anonymous

Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.

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• SciCrunch
• 14 years ago - by Anonymous

A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.

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• SciCrunch
• 14 years ago - by Anonymous

French university, located in Brest, in the Academy of Rennes.

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 1, 2022. Organization whose mission is to build and promote a sustainable ecosystem of professional societies, funding agencies, foundations, companies, and citizens together with life science researchers and innovators in computing, infrastructure and analysis with the expressed goal of translating new discoveries into tools, resources and products.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An annotated and searchable collection of protein sequences for the families of DNA-binding proteins. DnaProt maximizes family information retrieval and helps reveal the relationships within the various functional binding classes. This classification system, implemented in an web-based management resource, is available for online DNA-binding pattern search and specific DNA-binding record retrieval. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes.

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• SciCrunch
• 14 years ago - by Anonymous

A blog by the accomplished Yale Neurologist Steven Novella, MD, covering news and issues in neuroscience, but also general science, scientific skepticism, philosophy of science, critical thinking, and the intersection of science with the media and society. Dr. Novella is an academic clinical neurologist at Yale University School of Medicine. He is the president and co-founder of the New England Skeptical Society. He is the host and producer of the popular weekly science podcast, The Skeptics'' Guide to the Universe. He is also a senior fellow and Director of Science-Based Medicine at the James Randi Educational Foundation (JREF), a fellow of the Committee for Skeptical Inquiry (CSI) and a founding fellow of the Institute for Science in Medicine. Dr. Novella also contributes every Sunday to The Rogues Gallery, the official blog of the SGU, every Monday to SkepticBlog, and every Wednesday to Science-Based Medicine, a blog dedicated to issues of science and medicine.

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• SciCrunch
• 14 years ago - by Anonymous

A web program that can locate residue periodicities in either amino acid or DNA sequences. It is based on an algorithm of Dr. A.D. McLachlan (1977). NOTE: You must use a Java compatible browser to run the application.

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• SciCrunch
• 14 years ago - by Anonymous

A web tool to create, display and manipulate structures of small molecules, proteins and DNA.

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• SciCrunch
• 14 years ago - by Anonymous

An integrated environment designed to support protein sequence and structure analysis on the web.

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• SciCrunch
• 14 years ago - by Anonymous

A web tool to select biological sequences from a given set, with similarity / homology less than a user-defined level. This web-based application takes as input a set of N sequences and outputs a set of sequences of user-determined redundancy. Initially, the algorithm runs an all-against-all BLAST alignment on the input data set and creates an NxN matrix of pairwise distances defined by the similarity percentages. In the next step, the algorithm removes the sequence with the largest number of neighbors, causing that sequence not to be counted as a neighbor of any other sequence during the next iterations. It then reassesses the number of neighbors of each sequence and repeats the previous step until the sequences left over have no more neighbors. The user can specify the similarity (%) threshold and the minimum coverage length of the alignments. Sequences with a similarity below the threshold or a smaller coverage than the minimum length are not considered to be neighbors.

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• SciCrunch
• 14 years ago - by Anonymous

A web tool, based on a heuristic transformation of the original global pairwise and local pairwise alignment algorithms, offers objective alignments for transmembrane protein sequences. hPATM takes advantage of the information offered by the knowledge of the position of transmembrane segmets, by experiment or prediction. The heuristic approach may reveal similarities between diverge sequences with low percentages of identity and similarity. The produced alignments, based on common structural scaffolds derived by the transmembrane segments of the sequence, can be used to spot conserved non-transmembrane segments or as a basis for the production of 3-D models via homology modelling. The hPAFAG algorithm is based on the heuristic transformation of the Needleman & Wunsch and Smith & Waterman algorithms, featuring affine gap penalties. The heuristic transformation is based on two extra features: * a heuristic bonus, added to the score when two amino acids that belong to transmembrane segmens are aligned. * a heuristic gap penalty, substracted from the score when a gap is opened in a transmembrane segment. This way transmembrane segments are anchored (not by force, but by more strict alignment) together, allowing the pairwise alignment to focus on non-transmembrane segments. This web server offers a friendly interface for the hPATM command line version. The algorithm was implemented in PERL and the source code of the command line version is available on request by the authors.

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• SciCrunch
• 14 years ago - by Anonymous

A publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. Advanced data integration techniques make Human-gpDB very rich in context since all of the bioentities are linked to a rich variety of external data sources. High quality visualization methods make the networks more informative and the extraction of information easier. Human-gpDB is currently a very useful tool for drug targeting investigation. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors.

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• SciCrunch
• 14 years ago - by Anonymous

A relational database of Lepidoptera chorion proteins. The proteinaceous Lepidopteran chorions are used in our lab, as a model system towards unraveling the routes and rules of formation of natural protective amyloids. Therefore, we constructed LepChorionDB a relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was based on multiple sequence alignments of conserved key residues, in the central domain of, well characterized, silkmoth chorion proteins. These alignments were used to build Hidden Markov Models in order to search various DataBases. This work was a collaboration of the Department of Cell Biology and Biophysics, University of Athens and the Centre of Immunology & Transplantation Biomedical Research Foundation, Academy of Athens.

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• SciCrunch
• 14 years ago - by Anonymous