PubChem in 2021: new data content and improved web interfaces.
Sunghwan Kim,Jie Chen,Tiejun Cheng,Asta Gindulyte,Jia He,Siqian He,Qingliang Li,Benjamin A. Shoemaker,Paul A. Thiessen,Bo Yu,Leonid Zaslavsky,Jian Zhang,Evan E Bolton +12 more
Reads0
Chats0
TLDR
In the past two years, PubChem made substantial improvements, including a data model change for the data objects used by these pages as well as by programmatic users, and several new services were introduced.Abstract:
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).read more
Citations
More filters
Journal ArticleDOI
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties
Guo-Li Xiong,Zhenxing Wu,Jiacai Yi,Li Fu,Zhi-Jiang Yang,Chang-Yu Hsieh,Ming-Zhu Yin,Xiangxiang Zeng,Chengkun Wu,Aiping Lu,Chen Xiang,Tingjun Hou,Dong-Sheng Cao,Dong-Sheng Cao +13 more
TL;DR: ADMETlab 2.0 as discussed by the authors is a completely redesigned version of the widely used AMDETlab web server for the predictions of pharmacokinetics and toxicity properties of chemicals, of which the supported ADMET-related endpoints are approximately twice the number of the endpoints in the previous version, including 17 physicochemical properties, 13 medicinal chemistry properties, 23 ADME properties, 27 toxicity endpoints and 8 toxicophore rules.
Journal ArticleDOI
Artificial intelligence to deep learning: machine intelligence approach for drug discovery.
TL;DR: In this article, Artificial Neural Networks and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity.
Journal ArticleDOI
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents.
Ying Zhou,Yintao Zhang,Xichen Lian,Fengcheng Li,Chaoxin Wang,Feng Zhu,Yunqing Qiu,Yu Zong Chen,Yu Zong Chen +8 more
TL;DR: In this article, a major update of the Therapeutic Target Database, previously featured in NAR, was introduced, which includes poor binders and non-binders for developing discovery tools, prodrugs for improved therapeutics, co-targets of therapeutic targets for multi-target strategies and off-target investigations, and collective structureactivity and drug-likeness landscapes of enhanced drug feature.
Journal ArticleDOI
FlyBase: a guided tour of highlighted features
Madeline A. Crosby,Joshua L. Goodman,Thomas C. Kaufman,Aoife Larkin,Beverley B. Matthews,Victor B. Strelets,Norbert Perrimon,Susan Russo Gelbart,Kris Broll,Lynn Crosby,Gilberto dos Santos,Kathleen Falls,Victoria A. Jenkins,Ian Longden,J. P. Seme,Christopher J. Tabone,Pinglei Zhou,Mark Zytkovicz,Nicholas H. Brown,Giulia Antonazzo,Helen Attrill,Phani V. Garapati,Steven J Marygold,Alex D McLachlan,Arzu Öztürk-Çolak,Ch. Pilgrim,Vítor Trovisco,Brian R. Calvi,T. Kaufman,Pravija Krishna,Jim Thurmond,Richard M. Cripps,TyAnna L. Lovato +32 more
TL;DR: FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster, and the dedicated reports and tools it has constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities are emphasized.
Journal ArticleDOI
Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
Tia A. Tummino,Veronica V. Rezelj,Benoit Fischer,Audrey Fischer,Matthew J. O’Meara,Blandine Monel,Thomas Vallet,Kris M. White,Ziyang Zhang,Assaf Alon,Heiko Schadt,Henry R. O’Donnell,Jiankun Lyu,Romel Rosales,Briana L. McGovern,Raveen Rathnasinghe,Sonia Jangra,Michael Schotsaert,Jean-Rene Galarneau,Nevan J. Krogan,Laszlo Urban,Kevan M. Shokat,Andrew C. Kruse,Adolfo García-Sastre,Olivier Schwartz,Francesca Moretti,Marco Vignuzzi,Francois Pognan,Brian K. Shoichet +28 more
TL;DR: For example, this paper found that phospholipidosis was a shared mechanism underlying the antiviral activity of many repurposed drugs, including hydroxychloroquine, azithromycin, amiodarone, and four others already in clinical trials.
References
More filters
Journal ArticleDOI
Clinical Characteristics of Coronavirus Disease 2019 in China.
Wei-jie Guan,Zhengyi Ni,Yu Hu,Wenhua Liang,Chun-Quan Ou,Jianxing He,Lei Liu,Hong Shan,Chunliang Lei,David S.C. Hui,Bin Du,Lanjuan Li,Guang Zeng,Kowk-Yung Yuen,Ruchong Chen,Chun-Li Tang,Tao Wang,Ping-Yan Chen,Jie Xiang,Shiyue Li,Jinlin Wang,Zi-jing Liang,Yi-xiang Peng,Li Wei,Yong Liu,Ya-hua Hu,Peng Peng,Jian-ming Wang,Ji-yang Liu,Zhong Chen,Gang Li,Zhi-jian Zheng,Shao-qin Qiu,Jie Luo,Chang-jiang Ye,Shao-yong Zhu,Nanshan Zhong +36 more
TL;DR: During the first 2 months of the current outbreak, Covid-19 spread rapidly throughout China and caused varying degrees of illness, and patients often presented without fever, and many did not have abnormal radiologic findings.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area.
Safiya Richardson,Safiya Richardson,Jamie S. Hirsch,Jamie S. Hirsch,Mangala Narasimhan,James M. Crawford,Thomas McGinn,Thomas McGinn,Karina W. Davidson,Karina W. Davidson,Douglas P. Barnaby,Douglas P. Barnaby,Lance B Becker,John Chelico,John Chelico,Stuart L. Cohen,Stuart L. Cohen,Jennifer Cookingham,Kevin Coppa,Michael A Diefenbach,Andrew J. Dominello,Joan Duer-Hefele,Louise Falzon,Jordan Gitlin,Negin Hajizadeh,Negin Hajizadeh,Tiffany G. Harvin,David Hirschwerk,Eun Ji Kim,Eun Ji Kim,Zachary Kozel,Lyndonna Marrast,Lyndonna Marrast,Jazmin N. Mogavero,Gabrielle A. Osorio,Michael Qiu,Theodoros P. Zanos +36 more
TL;DR: This case series provides characteristics and early outcomes of sequentially hospitalized patients with confirmed COVID-19 in the New York City area and assesses outcomes during hospitalization, such as invasive mechanical ventilation, kidney replacement therapy, and death.
Journal ArticleDOI
The Reactome Pathway Knowledgebase.
Antonio Fabregat,Konstantinos Sidiropoulos,Phani V. Garapati,Marc Gillespie,Marc Gillespie,Kerstin Hausmann,Robin Haw,Bijay Jassal,S Jupe,Florian Korninger,Sheldon J. McKay,Lisa Matthews,Bruce May,Marija Milacic,Karen Rothfels,Veronica Shamovsky,Marissa Webber,Joel Weiser,Mark Williams,Guanming Wu,Lincoln Stein,Lincoln Stein,Lincoln Stein,Henning Hermjakob,Henning Hermjakob,Peter D'Eustachio +25 more
TL;DR: The Reactome Knowledgebase provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a single consistent data model.
Related Papers (5)
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more