In silico methods and tools for drug discovery

Zanubrutinib: First Approval

(2020) Yahiya Y. Syed   DRUGS

User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation

(2020) Bilal Shaker et al.   JOURNAL OF MICROBIOLOGY

Comparative Toxicogenomics Database (CTD): update 2021

(2020) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Identification of Potential Drug Targets in Helicobacter pylori Using In Silico Subtractive Proteomics Approaches and Their Possible Inhibition through Drug Repurposing

(2020) Kareem A. Ibrahim et al.   Pathogens

Open Targets Platform: supporting systematic drug–target identification and prioritisation

(2020) David Ochoa et al.   NUCLEIC ACIDS RESEARCH

3D-QSAR and molecular recognition of Klebsiella pneumoniae NDM-1 inhibitors

(2019) Huaichuan Duan et al.   MOLECULAR SIMULATION

A bright future for fragment-based drug discovery: what does it hold?

(2019) Célien Jacquemard et al.   Expert Opinion on Drug Discovery

MolTarPred: a web tool for comprehensive target prediction with reliability estimation

(2019) Antonio Peón et al.   Chemical Biology & Drug Design

QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models

(2019) Pravin Ambure et al.   Journal of Chemical Information and Modeling

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

Computational determination of hERG-related cardiotoxicity of drug candidates

(2019) Hyang-Mi Lee et al.   BMC BIOINFORMATICS

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Erdafitinib: First Global Approval

(2019) Anthony Markham   DRUGS

A Structure-Based Drug Discovery Paradigm

(2019) Maria Batool et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Apalutamide: A Review in Non-Metastatic Castration-Resistant Prostate Cancer

(2019) Zaina T. Al-Salama   DRUGS

Selinexor: First Global Approval

(2019) Yahiya Y. Syed   DRUGS

Computational/in silico methods in drug target and lead prediction

(2019) Francis E Agamah et al.   BRIEFINGS IN BIOINFORMATICS

Rational design of novel TLR4 ligands by in silico screening and their functional and structural characterization in vitro

(2018) Jan Honegr et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Identification of natural inhibitors against Acinetobacter baumannii d -alanine- d -alanine ligase enzyme: A multi-spectrum in silico approach

(2018) Sajjad Ahmad et al.   JOURNAL OF MOLECULAR LIQUIDS

ProTox-II: a webserver for the prediction of toxicity of chemicals

(2018) Priyanka Banerjee et al.   NUCLEIC ACIDS RESEARCH

CASTp 3.0: computed atlas of surface topography of proteins

(2018) Wei Tian et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database

(2018) Jie Dong et al.   Journal of Cheminformatics

Target deconvolution from phenotype-based drug discovery by using chemical proteomics approaches

(2018) Kazuishi Kubota et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Computer-aided drug discovery: Novel 3,9-disubstituted eudistomin U derivatives as potent antibacterial agents

(2018) Jiangkun Dai et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Editorial: Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems – Recent Developments and Advanced Applications

(2018) Thomas S. Hofer et al.   Frontiers in Chemistry

A New Approach for Drug Target and Bioactivity Prediction: The Multifingerprint Similarity Search Algorithm (MuSSeL)

(2018) Domenico Alberga et al.   Journal of Chemical Information and Modeling

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Open Targets Platform: new developments and updates two years on

(2018) Denise Carvalho-Silva et al.   NUCLEIC ACIDS RESEARCH

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

New active leads for tuberculosis booster drugs by structure-based drug discovery

(2017) Natalie J. Tatum et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data

(2017) Mahendra Awale et al.   Journal of Cheminformatics

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

(2017) Anna Cichonska et al.   PLoS Computational Biology

vNN Web Server for ADMET Predictions

(2017) Patric Schyman et al.   Frontiers in Pharmacology

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

(2017) Antoine Daina et al.   Scientific Reports

A multiple kernel learning algorithm for drug-target interaction prediction

(2016) André C. A. Nascimento et al.   BMC BIOINFORMATICS

General Ser/Thr Kinases Pharmacophore Approach for Selective Kinase Inhibitors Search as Exemplified by Design of Potent and Selective Aurora A Inhibitors

(2016) Natalya I. Vasilevich et al.   Chemical Biology & Drug Design

Descriptors and their selection methods in QSAR analysis: paradigm for drug design

(2016) Danishuddin et al.   DRUG DISCOVERY TODAY

Advances in structure-based drug discovery of carbonic anhydrase inhibitors

(2016) Claudiu T. Supuran   Expert Opinion on Drug Discovery

Determination of corrosion inhibition effects of amino acids: Quantum chemical and molecular dynamic simulation study

(2016) Savaş Kaya et al.   Journal of the Taiwan Institute of Chemical Engineers

The ways and means of fragment-based drug design

(2016) Bradley C. Doak et al.   PHARMACOLOGY & THERAPEUTICS

QSAR Toolbox – workflow and major functionalities

(2016) S. D. Dimitrov et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Computational approaches in target identification and drug discovery

(2016) Theodora Katsila et al.   Computational and Structural Biotechnology Journal

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

(2015) Elizabeth Brunk et al.   CHEMICAL REVIEWS

Fragment-Based Drug Discovery and Molecular Docking in Drug Design

(2015) Tao Wang et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

A low-cost, high-quality new drug discovery process using patient-derived induced pluripotent stem cells

(2015) Shibashish Giri et al.   DRUG DISCOVERY TODAY

Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation

(2015) Nidhi Singh et al.   Journal of Chemical Information and Modeling

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

I-TASSER server: new development for protein structure and function predictions

(2015) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Developing Enhanced Blood–Brain Barrier Permeability Models: Integrating External Bio-Assay Data in QSAR Modeling

(2015) Wenyi Wang et al.   PHARMACEUTICAL RESEARCH

Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis

(2015) Peter M. Njogu et al.   ACS Infectious Diseases

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Molecular Modeling on Streptolysin-O of Multidrug Resistant Streptococcus pyogenes and Computer Aided Screening and In Vitro Assay for Novel Herbal Inhibitors

(2014) Sinosh Skariyachan et al.   Current Computer-Aided Drug Design

Addressing toxicity risk when designing and selecting compounds in early drug discovery

(2014) Matthew D. Segall et al.   DRUG DISCOVERY TODAY

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

(2014) Soroosh Pezeshki et al.   MOLECULAR SIMULATION

Combating multidrug resistance in bacterial infection by targeting functional proteome with natural products

(2014) Meng Xiong et al.   NATURAL PRODUCT RESEARCH

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

(2014) David Gfeller et al.   NUCLEIC ACIDS RESEARCH

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on Chemogenomic Database

(2013) Lirong Wang et al.   AAPS Journal

HitPick: a web server for hit identification and target prediction of chemical screenings

(2013) X. Liu et al.   BIOINFORMATICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

DrugMint: a webserver for predicting and designing of drug-like molecules

(2013) Sandeep Kumar Dhanda et al.   Biology Direct

NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases

(2013) Dokyun Na et al.   BMC Medical Genomics

Farnesyl Diphosphate Synthase Inhibitors fromIn SilicoScreening

(2013) Steffen Lindert et al.   Chemical Biology & Drug Design

Editorial (Hot Topic: Computer-Aided Drug Design, Synthesis and Evaluation of New Anti-Cancer Drugs)

(2013) M. Natalia. D. S. Cordeiro et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Quantitative studies on structure–ORAC relationships of anthocyanins from eggplant and radish using 3D-QSAR

(2013) Pu Jing et al.   FOOD CHEMISTRY

Structure-based screening of inhibitors against KPC-2: designing potential drug candidates against multidrug-resistant bacteria

(2013) Mohd Danishuddin et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Hit Identification and Optimization in Virtual Screening: Practical Recommendations Based on a Critical Literature Analysis

(2013) Tian Zhu et al.   JOURNAL OF MEDICINAL CHEMISTRY

The 'rule of three' for fragment-based drug discovery: where are we now?

(2013) Harren Jhoti et al.   NATURE REVIEWS DRUG DISCOVERY

ModBase, a database of annotated comparative protein structure models and associated resources

(2013) Ursula Pieper et al.   NUCLEIC ACIDS RESEARCH

In Silico Approach for Predicting Toxicity of Peptides and Proteins

(2013) Sudheer Gupta et al.   PLoS One

Fragment-Based Approaches in Drug Discovery and Chemical Biology

(2012) Duncan E. Scott et al.   BIOCHEMISTRY

Locally Weighted Learning Methods for Predicting Dose-Dependent Toxicity with Application to the Human Maximum Recommended Daily Dose

(2012) Ruifeng Liu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Fragment Based Drug Design: From Experimental to Computational Approaches

(2012) A. Kumar et al.   CURRENT MEDICINAL CHEMISTRY

Using Computer-aided Drug Design and Medicinal Chemistry Strategies in the Fight Against Diabetes

(2012) Evandro P. Semighini et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

(2012) LiHong Hu et al.   Journal of Chemical Theory and Computation

Computational discovery of putative quorum sensing inhibitors against LasR and RhlR receptor proteins of Pseudomonas aeruginosa

(2012) Angusamy Annapoorani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor

(2012) Markus K. Dahlgren et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis of Potent Inhibitors of β-Ketoacyl-Acyl Carrier Protein Synthase III as Potential Antimicrobial Agents

(2012) Yan Liu et al.   MOLECULES

Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design

(2012) Pramod C. Nair et al.   ACS Medicinal Chemistry Letters

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based drug design to augment hit discovery

(2011) Subha Kalyaanamoorthy et al.   DRUG DISCOVERY TODAY

Molecular docking of γ-sitosterol with some targets related to diabetes

(2011) Rangachari Balamurugan et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

SuperTarget goes quantitative: update on drug-target interactions

(2011) N. Hecker et al.   NUCLEIC ACIDS RESEARCH

Novel Allosteric Sites on Ras for Lead Generation

(2011) Barry J. Grant et al.   PLoS One

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

(2011) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP9 assessment of free modeling target predictions

(2011) Lisa Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Critical Comparative Assessment of Predictions of Protein-Binding Sites for Biologically Relevant Organic Compounds

(2011) Ke Chen et al.   STRUCTURE

From 3D cell culture to organs-on-chips

(2011) Dongeun Huh et al.   TRENDS IN CELL BIOLOGY

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir

(2011) Li Xie et al.   PLoS Computational Biology

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

(2010) Bin Chen et al.   BMC BIOINFORMATICS

Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic

(2010) Tanaji Talele et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

3D-QSAR in Drug Design - A Review

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

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

(2010) Hanna Geppert et al.   Journal of Chemical Information and Modeling

Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields

(2010) Paolo Tosco et al.   JOURNAL OF MOLECULAR MODELING

Structure-Based Approaches to Target Fishing and Ligand Profiling

(2010) Didier Rognan   Molecular Informatics

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

(2010) Xiaofeng Liu et al.   NUCLEIC ACIDS RESEARCH

In silico discovery of 2-amino-4-(2,4-dihydroxyphenyl)thiazoles as novel inhibitors of DNA gyrase B

(2009) Matjaž Brvar et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Homology modeling in drug discovery: current trends and applications

(2009) Claudio N. Cavasotto et al.   DRUG DISCOVERY TODAY

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

(2009) Andreas Bender et al.   Journal of Chemical Information and Modeling

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure-Based Drug Design of Novel Aurora Kinase A Inhibitors: Structural Basis for Potency and Specificity

(2009) Mohane Selvaraj Coumar et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Myc−Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model

(2009) Gabriela Mustata et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Molecular docking and ligand specificity in fragment-based inhibitor discovery

(2009) Yu Chen et al.   Nature Chemical Biology

Identifying the proteins to which small-molecule probes and drugs bind in cells

(2009) S.-E. Ong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent advances and method development for drug target identification

(2009) Janet N.Y. Chan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

(2008) Weiguo Liu et al.   COMPUTER PHYSICS COMMUNICATIONS

Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery

(2008) Santiago Vilar et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery of Nonsteroidal 17β-Hydroxysteroid Dehydrogenase 1 Inhibitors by Pharmacophore-Based Screening of Virtual Compound Libraries

(2008) Daniela Schuster et al.   JOURNAL OF MEDICINAL CHEMISTRY

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested by Ab Initio QM/MM Molecular Dynamics Simulations

(2008) Po Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Do SET-Domain Protein Lysine Methyltransferases Achieve the Methylation State Specificity? Revisited by Ab Initio QM/MM Molecular Dynamics Simulations

(2008) Po Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SuperPred: drug classification and target prediction

(2008) M. Dunkel et al.   NUCLEIC ACIDS RESEARCH

The Contributions of Paul Ehrlich to Pharmacology: A Tribute on the Occasion of the Centenary of His Nobel Prize

(2008) Fèlix Bosch et al.   PHARMACOLOGY

A review of high throughput technology for the screening of natural products

(2007) K.P. Mishra et al.   BIOMEDICINE & PHARMACOTHERAPY

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins

(2007) Yeturu Kalidas et al.   JOURNAL OF STRUCTURAL BIOLOGY