Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

(2021) Giulia Fiscon et al.   PLoS Computational Biology

SAveRUNNER: an R-based tool for drug repurposing

(2021) Giulia Fiscon et al.   BMC BIOINFORMATICS

Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data

(2021) Andreas Bender et al.   DRUG DISCOVERY TODAY

In silico identification of prolyl hydroxylase inhibitor by per‐residue energy decomposition‐based pharmacophore approach

(2021) Mahesh Kumar Teli et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Target-Based Evaluation of “Drug-Like” Properties and Ligand Efficiencies

(2021) Paul D. Leeson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Exploring protein hotspots by optimized fragment pharmacophores

(2021) Dávid Bajusz et al.   Nature Communications

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

(2020) Fengcheng Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic Exploration of Activity Cliffs Containing Privileged Substructures

(2020) Huabin Hu et al.   MOLECULAR PHARMACEUTICS

ThETA: Transcriptome-driven Efficacy estimates for gene-based TArget discovery

(2020) Mario Failli et al.   BIOINFORMATICS

An open-source drug discovery platform enables ultra-large virtual screens

(2020) Christoph Gorgulla et al.   NATURE

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases

(2020) Rahil Taujale et al.   eLife

A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond

(2020) A K M Azad et al.   BRIEFINGS IN BIOINFORMATICS

Comparing a Query Compound with Drug Target Classes Using 3D-Chemical Similarity

(2020) Sang-Hyeok Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations

(2020) Pablo Herrera-Nieto et al.   Journal of Chemical Information and Modeling

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2020) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Activity cliffs produced by single-atom modification of active compounds: Systematic identification and rationalization based on X-ray structures

(2020) Huabin Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Machine-learning–driven biomarker discovery for the discrimination between allergic and irritant contact dermatitis

(2020) Vittorio Fortino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repurposing of FDA approved ring systems through bi-directional target-ring system dual screening

(2020) Surendra Kumar et al.   Scientific Reports

Exploration of Target Synergy in Cancer Treatment by Cell-Based Screening Assay and Network Propagation Analysis

(2019) J. Jesús Naveja et al.   Journal of Chemical Information and Modeling

Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

(2019) Jing Tang et al.   MOLECULAR & CELLULAR PROTEOMICS

Tracing the origin and evolution of pseudokinases across the tree of life

(2019) Annie Kwon et al.   Science Signaling

From Target to Drug: Generative Modeling for the Multimodal Structure-Based Ligand Design

(2019) Miha Skalic et al.   MOLECULAR PHARMACEUTICS

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

(2019) Ann Lin et al.   Science Translational Medicine

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

(2019) Valerio Licursi et al.   BMC BIOINFORMATICS

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

An omics perspective on drug target discovery platforms

(2019) Jussi Paananen et al.   BRIEFINGS IN BIOINFORMATICS

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

The expanding role of prodrugs in contemporary drug design and development

(2018) Jarkko Rautio et al.   NATURE REVIEWS DRUG DISCOVERY

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

(2018) Ying Hong Li et al.   BRIEFINGS IN BIOINFORMATICS

Drug discovery effectiveness from the standpoint of therapeutic mechanisms and indications

(2017) Hsin-Pei Shih et al.   NATURE REVIEWS DRUG DISCOVERY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

A comprehensive map of molecular drug targets

(2016) Rita Santos et al.   NATURE REVIEWS DRUG DISCOVERY

Harnessing benefit from targeting tumor associated carbohydrate antigens

(2016) Thomas Kieber-Emmons et al.   Human Vaccines & Immunotherapeutics

Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs

(2015) Lin Tao et al.   PHARMACOLOGICAL RESEARCH

Exploring Activity Cliffs in Medicinal Chemistry

(2012) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

Large-scale prediction and testing of drug activity on side-effect targets

(2012) Eugen Lounkine et al.   NATURE

Quantifying the chemical beauty of drugs

(2012) G. Richard Bickerton et al.   Nature Chemistry

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Imidazolopiperazines: Hit to Lead Optimization of New Antimalarial Agents

(2011) Tao Wu et al.   JOURNAL OF MEDICINAL CHEMISTRY

3D-QSAR in Drug Design - A Review

(2010) Jitender Verma et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

(2010) Daniel Seeliger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor

(2008) L.Y. Han et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING