Peter Gund - Academia.edu (original) (raw)

Papers by Peter Gund

Research paper thumbnail of Computer-Assisted Synthetic Analysis in Drug Research

ACS Symposium Series, 1977

Research paper thumbnail of Molecular modeling software and methods for medicinal chemistry

Journal of Medicinal Chemistry, 1990

Research paper thumbnail of Embracing complexity in drug discovery

Current opinion in drug discovery & development, 2007

Research paper thumbnail of BioAssay Templates for the Semantic Web 2 3

Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descri... more 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 be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a bioassay template data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.

Research paper thumbnail of ChemInform Abstract: THE NH2 SUBSTITUENT EFFECT ON THE PROPERTIES OF IONIC COMPOUNDS

Chemischer Informationsdienst, 1975

Research paper thumbnail of Chapter 27 Molecular Modeling as an Aid to Drug Design and Discovery

Annual Reports in Medicinal Chemistry, 1987

Publisher Summary This chapter discusses significant recent applications of this methodology and ... more Publisher Summary This chapter discusses significant recent applications of this methodology and some promising new developments. Recent bibliographies of molecular graphics and of theoretical calculations in molecular pharmacology contain more complete sets of references relevant to drug design and discovery. The chapter discusses molecular modeling studies of bioactive conformations of drugs; of 3D pharmacophore patterns, particularly for receptor agonists and antagonists; of inhibitor design, particularly when a 3D enzyme structure is available; of receptor mapping; and, finally, of protein and genetic engineering. The computational aids to drug design surveyed here are growing in sophistication, in relevance to “real-world” medicinal chemical research problems and in dissemination into the working pharmaceutical research environment. A number of enzyme and other macromolecular structures are becoming available from X-ray crystallography. Logically, these structures continue to be exploited in design of potential enzyme inhibitors. A systematic computational method for “screening” rigid ligands (taken from a data base of 3D structures) for complementarity of shape to an enzyme active site has been developed, as well as a method for allowing partial conformational flexibility in the “docking” process. Major current and future trends include reduction of hardware and software cost for using these methods, increased ease of use, and integration of these programs with other computational chemistry applications, such as chemical and biological data handling.

Research paper thumbnail of Additions and Corrections - The Synthesis of Cyclic Silicon Systems

Journal of the American Chemical Society, 1964

Research paper thumbnail of Guidelines for publications in molecular modeling related to medicinal chemistry

Journal of Medicinal Chemistry, 1988

Research paper thumbnail of Software Program Title:  Molecular Conceptor Drug Design Courseware. Version 1.02 By Claude Cohen. Synergix Ltd., Jerusalem, Israel. August, 2002. CD-ROM (plus HASP key, table of contents, and installation guide). ISBN 965-90508-0-1. <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mn>4900</mn><mo stretchy="false">(</mo><mi>c</mi><mi>o</mi><mi>m</mi><mi>m</mi><mi>e</mi><mi>r</mi><mi>c</mi><mi>i</mi><mi>a</mi><mi>l</mi><mo stretchy="false">)</mo><mo separator="true">,</mo></mrow><annotation encoding="application/x-tex">4900 (commercial), </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord">4900</span><span class="mopen">(</span><span class="mord mathnormal">co</span><span class="mord mathnormal">mm</span><span class="mord mathnormal">erc</span><span class="mord mathnormal">ia</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mclose">)</span><span class="mpunct">,</span></span></span></span>2900 (academic)

Journal of Medicinal Chemistry, 2003

Research paper thumbnail of Software Program Title: Molecular Conceptor Drug Design Courseware. Version 1.02 By Claude Cohen. Synergix Ltd., Jerusalem, Israel. August, 2002. CD-ROM (plus HASP key, table of contents, and installation guide). ISBN 965-90508-0-1. <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mn>4900</mn><mo stretchy="false">(</mo><mi>c</mi><mi>o</mi><mi>m</mi><mi>m</mi><mi>e</mi><mi>r</mi><mi>c</mi><mi>i</mi><mi>a</mi><mi>l</mi><mo stretchy="false">)</mo><mo separator="true">,</mo></mrow><annotation encoding="application/x-tex">4900 (commercial), </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord">4900</span><span class="mopen">(</span><span class="mord mathnormal">co</span><span class="mord mathnormal">mm</span><span class="mord mathnormal">erc</span><span class="mord mathnormal">ia</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mclose">)</span><span class="mpunct">,</span></span></span></span>2900 (academic)

Research paper thumbnail of Divisions of Chemical Information and Computers in Chemistry--symposia

IDrugs : the investigational drugs journal, 2000

Research paper thumbnail of ChemInform Abstract: On the Utility of Computational Methods for New Drug Discovery Projects

ChemInform, 1993

ABSTRACT ChemInform is a weekly Abstracting Service, delivering concise information at a glance t... more ABSTRACT ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Research paper thumbnail of Book Review of Chemoinformatics Approaches to Virtual Screening Chemoinformatics Approaches to Virtual Screening . Edited by Alexander Varnek and Alexander Tropsha . Royal Society of Chemistry, Cambridge, U.K. 2008 . ix + 342 pp. 16 × 24 cm. ISBN 9780854041442 . £89.95

Journal of Medicinal Chemistry, 2009

This is the 49th volume of this review series. A variety of timely topics is covered in 19 review... more This is the 49th volume of this review series. A variety of timely topics is covered in 19 reviews written by experts working in their respective fields. The reviews offer perspective and updates covering a broad range of individual topics in pharmacology and toxicology. Each individual review will be of value to medicinal chemists working in the scientific areas directly related to the given review topic. Select reviews that more directly address significant aspects of drug design/ discovery and are thus likely to be of more direct interest to medicinal chemists and those involved in drug discovery include: (1) Pharmacology of Nicotine: Addiction, Smoking-Induced Disease, and Therapeutics; (2) Lipid Mediators in Health and Disease: Enzymes and Receptors as Therapeutic Targets for the Regulation of Immunity and Inflammation; (3) Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction to Reactivate p53 Function: A Novel Approach for Cancer Therapy; (4) Epigenics, DNA Methylation, and Chromatin Modifying Drugs; (5) The COXIB Experience: A Look in the Rearview Mirror; (6) Immunodrugs: Therapeutic VLP-Based Vaccines for Chronic Diseases; (7) Topical Microbicides to Prevent HIV: Clinical Drug Development Challenges; (8) Emerging Pharmacology: Inhibitors of Human Immunodeficiency Virus Integration; (9) Mycobacterial Subversion of Chemotherapeutic Reagents and Host Defense Tactics: Challenges in Tuberculosis Drug Development. All reviews are cohesive and informative. The subject index is complete and thorough. Citations for most reviews are substantial and current. The present volume is a welcome addition to this long-standing series, providing concise summaries of advances in Pharmacology and Toxicology. It is noteworthy that this book, as well as additional Annual Reviews series, is located online at www.annualreviews.org.

Research paper thumbnail of Chemoinformatics in Drug Discovery. Methods and Principles in Medicinal Chemistry. Volume 23 Edited by R. Mannhold, H. Kubinyi, and G. Folkers. Wiley-VCH Verlag GmbH, Weinheim, Germany. 2005. xxii + 493 pp. 17 × 25 cm. ISBN 3-5273-0753-2. $185.00

Journal of Medicinal Chemistry, 2005

Research paper thumbnail of Bioinformatics and Drug Discovery. Methods in Molecular Biology. Volume 316 Edited by Richard S. Larson. Humana Press, Totowa, NJ. 2005. x + 444 pp. 16 × 23 cm. ISBN 1-588-29-346-7. $125.00

Journal of Medicinal Chemistry, 2006

Research paper thumbnail of Book Review of Functional Informatics in Drug Discovery Functional Informatics in Drug Discovery . Edited by Sergey Ilyin . CRC Press, Taylor & Francis Group, Boca Raton, FL 2008 . xii + 146 pp. 16 × 24 cm. ISBN 978-1-57444-466-7. $99.95

Journal of Medicinal Chemistry, 2008

Research paper thumbnail of Book Review of Functional Informatics in Drug Discovery Functional Informatics in Drug Discovery . Edited by Sergey Ilyin . CRC Press, Taylor & Francis Group, Boca Raton, FL 2008 . xii + 146 pp. 16 × 24 cm. ISBN 978-1-57444-466-7. $99.95

Journal of Medicinal Chemistry, 2008

Research paper thumbnail of Amino substituent effect on the properties of ionic compounds

Research paper thumbnail of Congestion. Conformation-dependent measure of steric environment. Derivation and application in stereoselective addition to unsaturated carbon

Research paper thumbnail of Can we help one billion sick people?

Current Opinion in Drug Discovery Development, Jun 1, 2008

Research paper thumbnail of Computer-Assisted Synthetic Analysis in Drug Research

ACS Symposium Series, 1977

Research paper thumbnail of Molecular modeling software and methods for medicinal chemistry

Journal of Medicinal Chemistry, 1990

Research paper thumbnail of Embracing complexity in drug discovery

Current opinion in drug discovery & development, 2007

Research paper thumbnail of BioAssay Templates for the Semantic Web 2 3

Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descri... more 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 be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a bioassay template data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.

Research paper thumbnail of ChemInform Abstract: THE NH2 SUBSTITUENT EFFECT ON THE PROPERTIES OF IONIC COMPOUNDS

Chemischer Informationsdienst, 1975

Research paper thumbnail of Chapter 27 Molecular Modeling as an Aid to Drug Design and Discovery

Annual Reports in Medicinal Chemistry, 1987

Publisher Summary This chapter discusses significant recent applications of this methodology and ... more Publisher Summary This chapter discusses significant recent applications of this methodology and some promising new developments. Recent bibliographies of molecular graphics and of theoretical calculations in molecular pharmacology contain more complete sets of references relevant to drug design and discovery. The chapter discusses molecular modeling studies of bioactive conformations of drugs; of 3D pharmacophore patterns, particularly for receptor agonists and antagonists; of inhibitor design, particularly when a 3D enzyme structure is available; of receptor mapping; and, finally, of protein and genetic engineering. The computational aids to drug design surveyed here are growing in sophistication, in relevance to “real-world” medicinal chemical research problems and in dissemination into the working pharmaceutical research environment. A number of enzyme and other macromolecular structures are becoming available from X-ray crystallography. Logically, these structures continue to be exploited in design of potential enzyme inhibitors. A systematic computational method for “screening” rigid ligands (taken from a data base of 3D structures) for complementarity of shape to an enzyme active site has been developed, as well as a method for allowing partial conformational flexibility in the “docking” process. Major current and future trends include reduction of hardware and software cost for using these methods, increased ease of use, and integration of these programs with other computational chemistry applications, such as chemical and biological data handling.

Research paper thumbnail of Additions and Corrections - The Synthesis of Cyclic Silicon Systems

Journal of the American Chemical Society, 1964

Research paper thumbnail of Guidelines for publications in molecular modeling related to medicinal chemistry

Journal of Medicinal Chemistry, 1988

Research paper thumbnail of Software Program Title:  Molecular Conceptor Drug Design Courseware. Version 1.02 By Claude Cohen. Synergix Ltd., Jerusalem, Israel. August, 2002. CD-ROM (plus HASP key, table of contents, and installation guide). ISBN 965-90508-0-1. <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mn>4900</mn><mo stretchy="false">(</mo><mi>c</mi><mi>o</mi><mi>m</mi><mi>m</mi><mi>e</mi><mi>r</mi><mi>c</mi><mi>i</mi><mi>a</mi><mi>l</mi><mo stretchy="false">)</mo><mo separator="true">,</mo></mrow><annotation encoding="application/x-tex">4900 (commercial), </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord">4900</span><span class="mopen">(</span><span class="mord mathnormal">co</span><span class="mord mathnormal">mm</span><span class="mord mathnormal">erc</span><span class="mord mathnormal">ia</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mclose">)</span><span class="mpunct">,</span></span></span></span>2900 (academic)

Journal of Medicinal Chemistry, 2003

Research paper thumbnail of Software Program Title: Molecular Conceptor Drug Design Courseware. Version 1.02 By Claude Cohen. Synergix Ltd., Jerusalem, Israel. August, 2002. CD-ROM (plus HASP key, table of contents, and installation guide). ISBN 965-90508-0-1. <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mn>4900</mn><mo stretchy="false">(</mo><mi>c</mi><mi>o</mi><mi>m</mi><mi>m</mi><mi>e</mi><mi>r</mi><mi>c</mi><mi>i</mi><mi>a</mi><mi>l</mi><mo stretchy="false">)</mo><mo separator="true">,</mo></mrow><annotation encoding="application/x-tex">4900 (commercial), </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord">4900</span><span class="mopen">(</span><span class="mord mathnormal">co</span><span class="mord mathnormal">mm</span><span class="mord mathnormal">erc</span><span class="mord mathnormal">ia</span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mclose">)</span><span class="mpunct">,</span></span></span></span>2900 (academic)

Research paper thumbnail of Divisions of Chemical Information and Computers in Chemistry--symposia

IDrugs : the investigational drugs journal, 2000

Research paper thumbnail of ChemInform Abstract: On the Utility of Computational Methods for New Drug Discovery Projects

ChemInform, 1993

ABSTRACT ChemInform is a weekly Abstracting Service, delivering concise information at a glance t... more ABSTRACT ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Research paper thumbnail of Book Review of Chemoinformatics Approaches to Virtual Screening Chemoinformatics Approaches to Virtual Screening . Edited by Alexander Varnek and Alexander Tropsha . Royal Society of Chemistry, Cambridge, U.K. 2008 . ix + 342 pp. 16 × 24 cm. ISBN 9780854041442 . £89.95

Journal of Medicinal Chemistry, 2009

This is the 49th volume of this review series. A variety of timely topics is covered in 19 review... more This is the 49th volume of this review series. A variety of timely topics is covered in 19 reviews written by experts working in their respective fields. The reviews offer perspective and updates covering a broad range of individual topics in pharmacology and toxicology. Each individual review will be of value to medicinal chemists working in the scientific areas directly related to the given review topic. Select reviews that more directly address significant aspects of drug design/ discovery and are thus likely to be of more direct interest to medicinal chemists and those involved in drug discovery include: (1) Pharmacology of Nicotine: Addiction, Smoking-Induced Disease, and Therapeutics; (2) Lipid Mediators in Health and Disease: Enzymes and Receptors as Therapeutic Targets for the Regulation of Immunity and Inflammation; (3) Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction to Reactivate p53 Function: A Novel Approach for Cancer Therapy; (4) Epigenics, DNA Methylation, and Chromatin Modifying Drugs; (5) The COXIB Experience: A Look in the Rearview Mirror; (6) Immunodrugs: Therapeutic VLP-Based Vaccines for Chronic Diseases; (7) Topical Microbicides to Prevent HIV: Clinical Drug Development Challenges; (8) Emerging Pharmacology: Inhibitors of Human Immunodeficiency Virus Integration; (9) Mycobacterial Subversion of Chemotherapeutic Reagents and Host Defense Tactics: Challenges in Tuberculosis Drug Development. All reviews are cohesive and informative. The subject index is complete and thorough. Citations for most reviews are substantial and current. The present volume is a welcome addition to this long-standing series, providing concise summaries of advances in Pharmacology and Toxicology. It is noteworthy that this book, as well as additional Annual Reviews series, is located online at www.annualreviews.org.

Research paper thumbnail of Chemoinformatics in Drug Discovery. Methods and Principles in Medicinal Chemistry. Volume 23 Edited by R. Mannhold, H. Kubinyi, and G. Folkers. Wiley-VCH Verlag GmbH, Weinheim, Germany. 2005. xxii + 493 pp. 17 × 25 cm. ISBN 3-5273-0753-2. $185.00

Journal of Medicinal Chemistry, 2005

Research paper thumbnail of Bioinformatics and Drug Discovery. Methods in Molecular Biology. Volume 316 Edited by Richard S. Larson. Humana Press, Totowa, NJ. 2005. x + 444 pp. 16 × 23 cm. ISBN 1-588-29-346-7. $125.00

Journal of Medicinal Chemistry, 2006

Research paper thumbnail of Book Review of Functional Informatics in Drug Discovery Functional Informatics in Drug Discovery . Edited by Sergey Ilyin . CRC Press, Taylor & Francis Group, Boca Raton, FL 2008 . xii + 146 pp. 16 × 24 cm. ISBN 978-1-57444-466-7. $99.95

Journal of Medicinal Chemistry, 2008

Research paper thumbnail of Book Review of Functional Informatics in Drug Discovery Functional Informatics in Drug Discovery . Edited by Sergey Ilyin . CRC Press, Taylor & Francis Group, Boca Raton, FL 2008 . xii + 146 pp. 16 × 24 cm. ISBN 978-1-57444-466-7. $99.95

Journal of Medicinal Chemistry, 2008

Research paper thumbnail of Amino substituent effect on the properties of ionic compounds

Research paper thumbnail of Congestion. Conformation-dependent measure of steric environment. Derivation and application in stereoselective addition to unsaturated carbon

Research paper thumbnail of Can we help one billion sick people?

Current Opinion in Drug Discovery Development, Jun 1, 2008