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Barry A. Bunin
Collaborative Drug Discovery
28Publications
13H-index
597Citations
Publications 28
Newest
#1Alex M. Clark (Collaborative Drug Discovery)H-Index: 18
#2Leah McEwen (Cornell University)H-Index: 2
Last.Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
view all 4 authors...
We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill the same role for substances that are composed of multiple components as the venerable Molfile does for specifying individual structures. This much needed datastructure is intended to replace current practices for communicating information about mixtures, which usually relies on human-readable text descriptions, drawing several species wit...
#1Sean EkinsH-Index: 58
#2Alex M. Clark (Collaborative Drug Discovery)H-Index: 18
Last.Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
view all 9 authors...
#1Sean Ekins (Collaborative Drug Discovery)H-Index: 58
#2Anna Spektor (Collaborative Drug Discovery)H-Index: 2
Last.Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
view all 5 authors...
Neglected disease drug discovery is generally poorly funded compared with major diseases and hence there is an increasing focus on collaboration and precompetitive efforts such as public–private partnerships (PPPs). The More Medicines for Tuberculosis (MM4TB) project is one such collaboration funded by the EU with the goal of discovering new drugs for tuberculosis. Collaborative Drug Discovery has provided a commercial web-based platform called CDD Vault which is a hosted collaborative solution ...
#1Sean EkinsH-Index: 58
#2Alex M. ClarkH-Index: 18
Last.Antony J. WilliamsH-Index: 37
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The past decade has seen an increased availability of databases with both molecular structures and bioactivity (e.g. binding affinity data) curated from publications or submitted by high throughput screening centers. Early collections of curated data, such as BindingDB or ChemBank, were initially eclipsed by PubChem, ChEMBL and commercial literature databases. In 2016, there are now many smaller focused databases that are freely available, such as the GtoPdb and the public data in Collaborative ...
#1Alex M. Clark (Collaborative Drug Discovery)H-Index: 2
#2Nadia K. Litterman (Collaborative Drug Discovery)H-Index: 13
Last.Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
view all 6 authors...
Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object). With appropriate annotation, assays can...
#1Sean Ekins (Collaborative Drug Discovery)H-Index: 58
#2Nadia K. Litterman (Collaborative Drug Discovery)H-Index: 13
Last.Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
view all 4 authors...
Purpose We propose a framework with simple proxies to dissect the relative energy contributions responsible for standard drug discovery binding activity.
#1Sean Ekins (Collaborative Drug Discovery)H-Index: 58
#2Jair L. Siqueira-Neto (UM: University of Montana)H-Index: 15
Last.Michelle R. Arkin (UCSF: University of California, San Francisco)H-Index: 34
view all 13 authors...
© 2015 Ekins et al.Background Chagas disease is a neglected tropical disease (NTD) caused by the eukaryotic parasite Trypanosoma cruzi. The current clinical and preclinical pipeline for T. cruzi is extremely sparse and lacks drug target diversity. Methodol
In a decade with over half a billion dollars of investment, more than 300 chemical probes have been identified to have biological activity through NIH funded screening efforts. We have collected the evaluations of an experienced medicinal chemist on the likely chemistry quality of these probes based on a number of criteria including literature related to the probe and potential chemical reactivity. Over 20% of these probes were found to be undesirable. Analysis of the molecular properties of the...
#1Alex M. Clark (Collaborative Drug Discovery)H-Index: 2
#2Barry A. Bunin (Collaborative Drug Discovery)H-Index: 13
Last.Ubbo Visser (UM: University of Miami)H-Index: 19
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Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO) p...
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