Other links, diseases...

 

  • OncoSearch - Cancer gene search engine with literature evidence
  • Ageing - The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource
  • Fragment - Blog on fragment-based drug design, comments about PAINS. My personal view is warning about blogs in general. Many people use blog to destroy the work of others without knowing the study, without looking at the data..., in many blogs I do see some people teaching the rest of the world what is good and bad research, this is of little interest, I am not saying that this is the case on this blog, but I see many offending comments there about published articles, internet is free, people can say what they want, fine with me, but warning about this, we ll see in 10 to 20 years from now if this is really helping. For now, we are in the Bezdek's curve, it is hype to destroy some study and some chemical groups, then in some years most of this will vanish in the air, and then, finally something positive will come out
  • PAINS - Blog on PAINS compounds, just read my comments about blogs above and below, warning about the blablabla without real data at hand, so again 50% interesting, 50% offending the work of others... funny enough, many people on these blogs do not realize that the road to hell is paved with good intentions...I have heard so many times do this dont do that...Of course one has to learn from the past but we ll see in 10 to 20 years from now if such agitation was really necessary
  • IMP - A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks (2015) - online
  • Blog - Chemistry blog, comments as above about blogs, many people on these blogs want to teach us what to do and how to think, they believe they know everything but the way they write about other people's work just say one thing, they are frustrated scientists wanting to hurt, nothing to do with science, very often it sounds like propaganda...
  • Drug-drug - BEReX: Biomedical Entity-Relationship eXplorer. Allows users to find the shortest paths between two remote nodes, find the most relevant drugs, diseases, pathways and so on related to the current network, expand the network by particular types of entities and relations and modify the network by removing or adding selected nodes - standalone
  • PlateletWeb - A systems biologic analysis of signaling networks in human platelets (e.g, Search for a specific protein in the Platelet Interactome) - online
  • BioMart - The project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process
  • BioMart - Creative Biomart. Quantify Recombinant Proteins - commercial
  • Mouse - The mouse genome database. Genotypes, Phenotypes, and Models of Human Disease
  • Link - Prolific protein-literature investigation for interacting compounds
  • PHISTO - Pathogen-Host Interaction Search Tool - online
  • IDSA - Bad bugs, no drugs. The infectious disease society of America - online
  • ATC - The Anatomical Therapeutic Chemical classification system and the Defined Daily Dose (DDD) as a measuring unit have become the gold standard for international drug utilization research. WHO Collaborating Centre for Drug Statistics Methodology - online
  • DisGeNET - A new gene-disease database integrating gene-disease associations from several public, expert, curated data sources and text mining derived associations - online
  • BioLabeler - It extracts UMLS concepts from Biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be use to automatically curate and annotate BioMedical Literature or to index large documents databases and improve searches or discover relationships between them
  • Biomine - Integrates and indexes data from several publicly available biological databases with the aim of aiding explorative discovery of non-trivial connections between biological entities, such as genes and phenotypes - online
  • PubTator - It is a Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques
  • OSCAR - Open Source Chemistry Analysis Routines is an open source extensible system for the automated annotation of chemistry in scientific articles
  • OSDD - List of computer tools
  • PIE - Searching PubMed literature for protein interaction information
  • PRO - Provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them (target)
  • KiPar - It is a standalone Java application for the retrieval of textual documents likely to contain information relevant for kinetic modelling of a given metabolic pathway
  • eGIFT - Extracting Gene Information From Text - online
  • InterMine - Complex data integration (standalone)
  • EnrichNet - Network-based enrichment analysis Enter your gene/protein set of interest - online
  • MyMiner - A web application for computer-assisted biocuration and text annotation
  • OLSVis - A visual browser for EBI s OLS (Ontology Lookup Service) : a structured collection of terminology across various biological domains
  • Drugs - Top 100 drugs
  • Drugs - Poster: top 200 drugs
  • Patients - PatientsLikeMe. Share your experiences with treatments. Find patients just like you
  • ICTRP - International Clinical Trials Registry Platform. What is a clinical trial? What is trial registration? WHO
  • OBRC - Online Bioinformatics Resources Collection
  • Trialtrove - The world s most comprehensive real-time source of pharmaceutical clinical trials intelligence, gathering clinical trial information from over 20,000 clinical trial data sources to provide a continually updated reference of clinical trials research in more than 150 countries - database
  • EudraCT - A database of clinical trials in EU - database
  • Trials - ClinicalTrials at the FDA. A registry and results database of publicly and privately supported clinical studies of human participants conducted around the world (Trials) - database
  • FDA - FDA Post-Approval Studies - database
  • UK Biobank - UK Biobank is a major national health resource, with the aim of improving the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses, including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia. UK Biobank recruited 500,000 people aged between 40-69 years in 2006-2010 from across the country to take part in this project. They have undergone measures, provided blood, urine and saliva samples for future analysis, detailed information about themselves and agreed to have their health followed. Over many years this will build into a powerful resource to help scientists discover why some people develop particular diseases and others do not - database
  • Link - Protein level predictions 1 - Pathogenic or not
  • Click2drug - Directory of computer-aided Drug Design tools - Drug Design tools
  • P450 - Cytochrome P450 interactions - training CYP
  • Bioinfo - Resources on bioinformatics classified by categories
  • NCBI - NCBI database. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs - database
  • Variome - The human variome project. Currently working with the World Health Organization (WHO) and other partners on a consultation to determine the feasibility of establishing a global program on human genomics and public health
  • HapMap - The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals - database
  • dbSNP - dbSNP short genetic variation - database
  • JSNP - A database of common gene variations in the Japanese population - database
  • 1000 - 1000 genomes At NCBI - database
  • Pathguide - It contains information about 325 biological pathway related resources and molecular interaction related resources including Protein-Protein Interactions and many others - A pathway resource list
  • Chemistry - Sixty-Four Free Chemistry (and related) Databases - databases
  • PSICQUIC - View Links to multiple molecular interaction databases - databases
  • Bioinfo - Directory of curated Links to molecular resources, in silico tools and databases - List of tools essentially from NAR issues, tends to focus on bioinformatics, genomics but some tools are for drugs and structural bioinformatics
  • SCT - French Society for drug discovery      
  • SFCi - French Society of Chemoinformatics      
  • Biophysics - Links to the Theoretical and Computational Biophysics group - list of tools essentially for macromolecules      
  • oreChem - Project: Integrating Chemistry Scholarship with the Semantic Web
  • Software - Many tools for modeling and mining small molecules, proteins, DNA, RNA, partial charges...solvent accessible molecular surface area with MASKER...
  • Chemoinfo - Numerous info about chemoinformatics - chemoinformatics data set, IC50 on several targets
  • Computer tools - Numerous Links for chemistry and computer tools - Many chemistry Links by Dr. L P Taylor
  • PolySearch - PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more - online
  • iHOP - Information hyperLinked over proteins - online
  • ANNOVAR - An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes - standalone
  • Frisbi - FRENCH INFRASTRUCTURE FOR INTEGRATED STRUCTURAL BIOLOGY - international project structural biology
  • IPAD - the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (a new resource for analyzing, identifying, and validating pathway, disease, drug, organ specificity and their inter-associations) - database
  • Barcode - Barcode algorithm. It is designed to estimate which genes are expressed in tissues - database
  • FacPad - Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment - database
  • Net2.0 - ResponseNet2.0. Revealing signaling and regulatory pathways connecting your proteins and genes, now with human data - online
  • TCGA - The Cancer Genome Atlas - online
  • Last updated on .

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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira