AtlasCBS: a web server to map and explore chemico-biological space

Cortés-Cabrera, Álvaro; Morreale, Antonio; Gago, Federico; Abad‐Zapatero, Celerino

doi:10.1007/s10822-012-9587-5

Cited by 6 publications

(1 citation statement)

References 18 publications

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“…The complexity of biological systems and the subtleties of biochemistry, genetics and pharmacology prevent a direct 'optimization' path. Currently, after my retirement from Abbott Laboratories, I continue to explore ways to map chemico-biological space (AtlasCBS: https://www.ebi.ac.uk/chembl/atlascbs/intro.jsp) in ways that could be relevant to the pharmaceutical industry (Cortés-Cabrera et al, 2012;Abad-Zapatero, 2013b). I will only add that since chemistry is not my strongest background, I only see myself as a 'sorcerer's apprentice', when faced with the challenges of chemistry, biology, medicine and drug design.…”

Section: Sorcerer's Apprentice: Structure-based Drug Designmentioning

confidence: 99%

Celebrating macromolecular crystallography: A personal perspective

Abad‐Zapatero

2015

Arbor

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The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950's. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin) to the 'coming of age' of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists. KEYWORDS: crystallographic education; crystallography; history of macromolecular crystallography; international year of crystallography; origins of virus crystallography; Spanish education; Spanish research. RESUMEN:El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina), hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se reflexiona sobre el futuro de las próximas generaciones de científicos españoles.PALABRAS CLAVE: año internacional de la cristalografía; cristalografía; enseñanza de la cristalografía; educación en España; historia de la cristalografía macromolecular; investigación en España.

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Section: Sorcerer's Apprentice: Structure-based Drug Designmentioning

confidence: 99%

Celebrating macromolecular crystallography: A personal perspective

Abad‐Zapatero

2015

Arbor

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Progress on open chemoinformatic tools for expanding and exploring the chemical space

Medina-Franco

Sánchez-Cruz

López-López

et al. 2021

J Comput Aided Mol Des

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The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure–property relationships where the property can be a biological activity or any other characteristic of interest to a particular chemistry discipline. The chemical space is highly dependent on the molecular representation that is also a cornerstone concept in computational chemistry. Herein, we discuss the recent progress on chemoinformatic tools developed to expand and characterize the chemical space of compound data sets using different types of molecular representations, generate visual representations of such spaces, and explore structure–property relationships in the context of chemical spaces. We emphasize the development of methods and freely available tools focusing on drug discovery applications. We also comment on the general advantages and shortcomings of using freely available and easy-to-use tools and discuss the value of using such open resources for research, education, and scientific dissemination.

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The AtlasCBS Application

Abad‐Zapatero¹

2013

Ligand Efficiency Indices for Drug Discovery

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AtlasCBS: a web server to map and explore chemico-biological space

Cited by 6 publications

References 18 publications

Celebrating macromolecular crystallography: A personal perspective

Celebrating macromolecular crystallography: A personal perspective

Progress on open chemoinformatic tools for expanding and exploring the chemical space

The AtlasCBS Application

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