A5076510996- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Advanced Chemical Physics Studies
- Microbial Natural Products and Biosynthesis
- Metabolomics and Mass Spectrometry Studies
- Pharmacogenetics and Drug Metabolism
- Ammonia Synthesis and Nitrogen Reduction
- Chemical Reaction Mechanisms
- Molecular Junctions and Nanostructures
- SARS-CoV-2 and COVID-19 Research
- vaccines and immunoinformatics approaches
- Genetics, Bioinformatics, and Biomedical Research
- interferon and immune responses
- Mass Spectrometry Techniques and Applications
- Molecular Spectroscopy and Structure
- COVID-19 Clinical Research Studies
- Atmospheric chemistry and aerosols
- Microbial Community Ecology and Physiology
- Biomedical Text Mining and Ontologies
- Receptor Mechanisms and Signaling
- Genetic Associations and Epidemiology
- Gene Regulatory Network Analysis
- Genomics and Rare Diseases
- Cell Image Analysis Techniques
- Plant biochemistry and biosynthesis
European Bioinformatics Institute
2011-2023
Wellcome Trust
2010-2016
Open Targets
2016
Universidade Federal do Rio Grande do Norte
2015
Institute of Theoretical Physics
2007-2010
Vrije Universiteit Amsterdam
2005-2008
University of Girona
2008
ChEMBL is an Open Data database containing binding, functional and ADMET information for a large number of drug-like bioactive compounds. These data are manually abstracted from the primary published literature on regular basis, then further curated standardized to maximize their quality utility across wide range chemical biology drug-discovery research problems. Currently, contains 5.4 million bioactivity measurements more than 1 compounds 5200 protein targets. Access available through...
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside continued extraction of data from medicinal chemistry literature, new sources have also been added to database. These include: deposited sets neglected disease screening; crop protection data; drug metabolism disposition patents. A number improvements features incorporated. include annotation assays targets...
ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In last two years, several important improvements have been made to are here. These include more robust capture representation of assay details; new data deposition system, allowing updating sets supplementary data; completely redesigned web interface, with enhanced search filtering capabilities.
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 Nucleic Acids Research Database Issue. Since then, a variety of new data sources and improvements functionality have contributed to growth utility resource. In particular, more comprehensive tracking compounds from research stages through clinical development market provided inclusion United States Adopted Name applications; richer model for representing drug targets has been...
We have designed and developed a data integration visualization platform that provides evidence about the association of known potential drug targets with diseases. The is to support identification prioritization biological for follow-up. Each target linked disease using integrated genome-wide from broad range sources. either target-centric workflow identify diseases may be associated specific target, or disease-centric disease. Users can easily transition between these target- workflows....
The ChEMBL database is one of a number public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming are typically not standardised according to consistent rules. In order maintain the quality final and easily compare integrate same compound different sources it necessary for chemical structures in be appropriately standardised.
Abstract ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 2019 Nucleic Acids Research Database Issues. Since its introduction 2009, ChEMBL’s content has changed dramatically size diversity data types. Through incorporation multiple new datasets from depositors since update, now contains slightly more bioactivity...
Nucleophilic substitution is ubiquitous in chemistry and well studied. Nucleophilicity leaving-group ability have been related to various reactant properties, such as electronegativity, size, polarizability, others. Yet, the state-of-the-art some extent still phenomenological. Here, we try arrive at a straightforward, causal relationship between reactants' electronic structure their S(N)2 reactivity. To this end, explored potential energy surfaces of backside frontside reactions X(-) + CH3Y...
It is textbook knowledge that nucleophilic substitution at carbon (SN2@C) proceeds via a central reaction barrier which disappears in the corresponding silicon (SN2@Si). Here, we address question why from SN2@C to SN2@Si despite fact these processes are isostructural and isoelectronic. To this end, have explored analyzed potential energy surfaces (PES) of various Cl- + CR3Cl (R = H, CH3) SiR3Cl model reactions CH3, C2H5, OCH3). Our results show nature SN2 essence steric, but it can be...
Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability differentiate marketed drugs from compounds reported bind efficacious target or targets. Using ChEMBL version 26, a data set of 643 acting on 271 targets was assembled, comprising 1104 drug–target pairs having ≥100 published per target. Taking into account changes in physicochemical properties over time, analyzed according class, therapy area, route...
To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions chloride anion at carbon in chloromethane (S(N)2@C) and silicon chlorosilane (S(N)2@Si), we have explored these PESes using hierarchical series ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] combination with six Gaussian-type basis sets, up to g polarization. Relative energies stationary points are converged within 0.01 0.56 kcal/mol as function basis-set...
We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X− + CH3CH2X with X = F Cl. This has been used to evaluate performance 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, hybrid density-functional theory (DFT). The ab initio obtained by exploring PESs using a hierarchical series methods [up CCSD(T)] in combination Gaussian-type basis sets (up aug-cc-pVQZ)....
The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/ ) was established to generate therapeutic target evidence from genome-scale experiments and analyses. CTTV aims support the validity of targets by integrating existing newly-generated data. Data integration has been achieved in some resources mapping metadata such as disease phenotypes Experimental Factor Ontology (EFO). Additionally, relationship between ontology descriptions rare common diseases their...
Abstract We have theoretically studied the gas‐phase nucleophilic substitution at group‐14 atoms (S N 2@A) in model reactions of Cl − +AH 3 (A=C, Si, Ge, Sn, and Pb) using relativistic density functional theory (DFT) ZORA‐OLYP/TZ2P. Firstly, we wish to explore understand how reaction coordinate ζ, potential energy surfaces (PES) along vary as center attack changes from carbon heavier atoms. Secondly, a comparison between more common backside 2‐b) frontside pathway 2‐f) is performed. The S...
The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification novel 'targets', usually proteins that can be modulated by small molecule to cure or minimise effects disease. Of 20,000 currently reported as comprising human proteome, just under quarter these potentially known molecules Storing information in curated, actively maintained databases help researchers access current quickly. However with...
The challenge of translating the huge amount genomic and biochemical data into new drugs is a costly challenging task. Historically, there has been comparatively little focus on linking chemical worlds. To address this need, we have developed ChEMBL, an online resource small-molecule SAR (structure–activity relationship) data, which can be used to support biology, lead discovery target selection in drug discovery. database contains abstracted structures, properties biological activities for...
The safety of marketed drugs is an ongoing concern, with some the more frequently prescribed medicines resulting in serious or life-threatening adverse effects patients. Safety-related information for approved has been curated to include assignment toxicity class(es) based on their withdrawn status and/or black box warning described medicinal product labels. ChEMBL resource contains a wide range bioactivity data types, from early "Discovery" stage preclinical individual compounds through...
Abstract Background The ChEMBL database is one of a number public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming are typically not standardised according to consistent rules. In order maintain the quality final and easily compare integrate same compound different sources it necessary for chemical structures in be appropriately standardised. Results A curation pipeline has been developed using open source toolkit RDKit. It comprises...
ChEMBL is a large-scale drug discovery database containing bioactivity information primarily extracted from scientific literature. Due to the medicinal chemistry focus of journals which data are extracted, currently most direct value in field human health research. However, many use-cases for current set equally applicable other fields, such as crop protection research: example, identification chemical scaffolds active against particular target or endpoint, de-convolution potential targets...