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  1. Book ; Conference proceedings: Pacific Symposium on Biocomputing 2016

    Altman, Russ B.

    Kohala Coast, Hawaii, USA, 4-8 January 2016

    2016  

    Event/congress Pacific Symposium on Biocomputing (21., 2016, KohalaHawaii)
    Author's details edited by Russ B. Altman [und 5 weitere]
    Language English
    Size ix, 592 Seiten, Illustrationen, Diagramme
    Publisher World Scientific
    Publishing place New Jersey
    Publishing country United States
    Document type Book ; Conference proceedings
    HBZ-ID HT019226171
    ISBN 978-981-4749-40-4 ; 9789814749411 ; 981-4749-40-0 ; 9814749419
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2017 A 813 available for loan (reading room) Lesesaal EG

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  2. Book ; Conference proceedings: Pacific Symposium on Biocomputing 2014

    Altman, Russ B.

    Kohala Coast, Hawaii, USA, 3 - 7 January 2014

    2014  

    Event/congress Pacific Symposium on Biocomputing (19., 2014, KohalaHawaii)
    Author's details ed. by Russ B. Altman
    Language English
    Size VII, 426 S. : Ill., graph. Darst., Kt.
    Publisher World Scientific
    Publishing place New Jersey u.a.
    Publishing country United States
    Document type Book ; Conference proceedings
    HBZ-ID HT018344542
    ISBN 978-981-4596-34-3 ; 981-4596-34-5
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2014 A 4226 available for loan (reading room) Lesesaal EG

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  3. Book: Principles of pharmacogenetics and pharmacogenomics

    Altman, Russ B.

    2012  

    Title variant Pharmacogenetics and pharmacogenomics
    Author's details ed. by Russ B. Altman
    Keywords Pharmacogenetics ; Pharmacological Phenomena / genetics ; Pharmakogenetik
    Language English
    Size XII, 269 S. : Ill., graph. Darst., Kt.
    Publisher Cambridge Univ. Press
    Publishing place Cambridge u.a.
    Publishing country Great Britain
    Document type Book
    HBZ-ID HT017192362
    ISBN 978-0-521-88537-9 ; 0-521-88537-X
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2012 A 2250 order for loan Magazin

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  4. Article ; Online: A Holy Grail - The Prediction of Protein Structure.

    Altman, Russ B

    The New England journal of medicine

    2023  Volume 389, Issue 15, Page(s) 1431–1434

    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMcibr2307735
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.34: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  5. Book ; Online ; Conference proceedings: Biocomputing 2021:Proceedings of the Pacific Symposium

    Altman, Russ B / Hunter, Lawrence / Klein, Teri E / Murray, Tiffany / Dunker, A Keith / Ritchie, Marylyn D

    2020  

    Keywords Protein Interactions ; Metabolomics ; Biocomputing ; Computational Genetics ; Ontology ; Computational Proteomics ; Bioinformatics
    Size 1 electronic resource (380 pages)
    Publisher World Scientific Publishing Company
    Document type Book ; Online ; Conference proceedings
    Note English ; Open Access
    HBZ-ID HT021027525
    ISBN 9789811232701 ; 9811232709
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  6. Article: Databases of ligand-binding pockets and protein-ligand interactions.

    Carpenter, Kristy A / Altman, Russ B

    Computational and structural biotechnology journal

    2024  Volume 23, Page(s) 1320–1338

    Abstract: Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases ... ...

    Abstract Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
    Language English
    Publishing date 2024-03-24
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2024.03.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online ; Conference proceedings: Biocomputing 2020:Proceedings of the Pacific Symposium

    Altman, Russ B / Dunker, A Keith / Hunter, Lawrence / Ritchie, Marylyn D / Murray, Tiffany / Klein, Teri E

    2019  

    Abstract: The Pacific Symposium on Biocomputing (PSB) 2020 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. ... ...

    Abstract The Pacific Symposium on Biocomputing (PSB) 2020 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2020 will be held on January 3 -7, 2020 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2020 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputings hot topics. In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field
    Size 1 electronic resource (764 pages)
    Publisher World Scientific Publishing Company
    Document type Book ; Online ; Conference proceedings
    Note ENG ; Open Access
    HBZ-ID HT020324176
    ISBN 9789811215636 ; 9811215634
    DOI 10.1142/11698
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  8. Book ; Online ; Conference proceedings: Biocomputing 2019:Proceedings of the Pacific Symposium:Pacific Symposium on Biocomputing 2019

    Altman, Russ B / Dunker, A Keith / Hunter, Lawrence / Ritchie, Marylyn D / Murray, Tiffany / Klein, Teri E

    2018  

    Abstract: The Pacific Symposium on Biocomputing (PSB) 2019 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. ... ...

    Abstract The Pacific Symposium on Biocomputing (PSB) 2019 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2019 will be held on January 3 - 7, 2019 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2019 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputings hot topics. In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field
    Size 1 electronic resource (472 p.)
    Publisher World Scientific Publishing Co
    Document type Book ; Online ; Conference proceedings
    Note ENG ; Open Access
    HBZ-ID HT020101779
    ISBN 9789813279827 ; 9813279826
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  9. Article: Explainable protein function annotation using local structure embeddings.

    Derry, Alexander / Altman, Russ B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The rapid expansion of protein sequence and structure databases has resulted in a significant number of proteins with ambiguous or unknown function. While advances in machine learning techniques hold great potential to fill this annotation gap, current ... ...

    Abstract The rapid expansion of protein sequence and structure databases has resulted in a significant number of proteins with ambiguous or unknown function. While advances in machine learning techniques hold great potential to fill this annotation gap, current methods for function prediction are unable to associate global function reliably to the specific residues responsible for that function. We address this issue by introducing PARSE (Protein Annotation by Residue-Specific Enrichment), a knowledge-based method which combines pre-trained embeddings of local structural environments with traditional statistical techniques to identify enriched functions with residue-level explainability. For the task of predicting the catalytic function of enzymes, PARSE achieves comparable or superior global performance to state-of-the-art machine learning methods (F1 score > 85%) while simultaneously annotating the specific residues involved in each function with much greater precision. Since it does not require supervised training, our method can make one-shot predictions for very rare functions and is not limited to a particular type of functional label (e.g. Enzyme Commission numbers or Gene Ontology codes). Finally, we leverage the AlphaFold Structure Database to perform functional annotation at a proteome scale. By applying PARSE to the dark proteome-predicted structures which cannot be classified into known structural families-we predict several novel bacterial metalloproteases. Each of these proteins shares a strongly conserved catalytic site despite highly divergent sequences and global folds, illustrating the value of local structure representations for new function discovery.
    Language English
    Publishing date 2023-10-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.13.562298
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Using GPT-3 to Build a Lexicon of Drugs of Abuse Synonyms for Social Media Pharmacovigilance.

    Carpenter, Kristy A / Altman, Russ B

    Biomolecules

    2023  Volume 13, Issue 2

    Abstract: Drug abuse is a serious problem in the United States, with over 90,000 drug overdose deaths nationally in 2020. A key step in combating drug abuse is detecting, monitoring, and characterizing its trends over time and location, also known as ... ...

    Abstract Drug abuse is a serious problem in the United States, with over 90,000 drug overdose deaths nationally in 2020. A key step in combating drug abuse is detecting, monitoring, and characterizing its trends over time and location, also known as pharmacovigilance. While federal reporting systems accomplish this to a degree, they often have high latency and incomplete coverage. Social-media-based pharmacovigilance has zero latency, is easily accessible and unfiltered, and benefits from drug users being willing to share their experiences online pseudo-anonymously. However, unlike highly structured official data sources, social media text is rife with misspellings and slang, making automated analysis difficult. Generative Pretrained Transformer 3 (GPT-3) is a large autoregressive language model specialized for few-shot learning that was trained on text from the entire internet. We demonstrate that GPT-3 can be used to generate slang and common misspellings of terms for drugs of abuse. We repeatedly queried GPT-3 for synonyms of drugs of abuse and filtered the generated terms using automated Google searches and cross-references to known drug names. When generated terms for alprazolam were manually labeled, we found that our method produced 269 synonyms for alprazolam, 221 of which were new discoveries not included in an existing drug lexicon for social media. We repeated this process for 98 drugs of abuse, of which 22 are widely-discussed drugs of abuse, building a lexicon of colloquial drug synonyms that can be used for pharmacovigilance on social media.
    MeSH term(s) United States ; Humans ; Social Media ; Pharmacovigilance ; Alprazolam ; Natural Language Processing ; Substance-Related Disorders
    Chemical Substances Alprazolam (YU55MQ3IZY)
    Language English
    Publishing date 2023-02-18
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom13020387
    Database MEDical Literature Analysis and Retrieval System OnLINE

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