Molecular Docking: Shifting Paradigms in Drug Discovery

Evaluation of amides, carbamates, sulfonamides and ureas of 4-prop-2-ynylidenecycloalkylamine as potent, selective, and bioavailable negative allosteric modulators of metabotropic glutamate receptor 5.

(2019) Davide Graziani et al.   JOURNAL OF MEDICINAL CHEMISTRY

Bigger is better in virtual drug screens

(2019) David E. Gloriam   NATURE

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction

(2019) Mauro S. Nogueira et al.   Journal of Chemical Information and Modeling

Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies

(2019) Margherita Lapillo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Trends in clinical success rates and therapeutic focus

(2019) Helen Dowden et al.   NATURE REVIEWS DRUG DISCOVERY

In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA)

(2019) Luca Pinzi et al.   MOLECULES

Refinement and Rescoring of Virtual Screening Results

(2019) Giulio Rastelli et al.   Frontiers in Chemistry

Repurposing mosloflavone/5,6,7-trimethoxyflavone-resveratrol hybrids: Discovery of novel p38-α MAPK inhibitors as potent interceptors of macrophage-dependent production of proinflammatory mediators

(2019) Ahmed H.E. Hassan et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Molecular Docking for Prediction and Interpretation of Adverse Drug Reactions.

(2018) Heng Luo et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Advancing drug discovery via GPU-based deep learning

(2018) Erik Gawehn et al.   Expert Opinion on Drug Discovery

Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery

(2018) Nicholas Thomford et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH

(2018) Federico Comitani et al.   Journal of Chemical Theory and Computation

A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening

(2018) Julia B. Jasper et al.   Journal of Cheminformatics

In silico profiling of systemic effects of drugs to predict unexpected interactions

(2018) Sunyong Yoo et al.   Scientific Reports

Where is crystallography going?

(2018) Jonathan M. Grimes et al.   Acta Crystallographica Section D-Structural Biology

Homology Modeling in Drug Discovery: Overview, Current Applications and Future Perspectives

(2018) Muhammed Tilahun Muhammed et al.   Chemical Biology & Drug Design

Parallelization of Molecular Docking: A Review

(2018) Dong Dong et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Selection of protein conformations for structure-based polypharmacology studies

(2018) Luca Pinzi et al.   DRUG DISCOVERY TODAY

Binding Affinity via Docking: Fact and Fiction

(2018) Tatu Pantsar et al.   MOLECULES

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

(2018) Rashmi R. Hazarika et al.   PLoS One

Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets

(2018) Nathalie Lagarde et al.   Oncotarget

Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations

(2018) Hari Leontiadou et al.   Scientific Reports

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

(2018) Isabella A. Guedes et al.   Frontiers in Pharmacology

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

(2018) Veronica Salmaso et al.   Frontiers in Pharmacology

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

(2018) Ashutosh Kumar et al.   Frontiers in Chemistry

Using a Consensus Docking Approach to Predict Adverse Drug Reactions in Combination Drug Therapies for Gulf War Illness

(2018) Rajeev Jaundoo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research

(2017) Nanyi Wang et al.   Journal of Chemical Information and Modeling

Computational Multitarget Drug Design

(2017) Weilin Zhang et al.   Journal of Chemical Information and Modeling

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

(2017) Xianjin Xu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A cross docking pipeline for improving pose prediction and virtual screening performance

(2017) Ashutosh Kumar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Dynamic Docking: A Paradigm Shift in Computational Drug Discovery

(2017) Dario Gioia et al.   MOLECULES

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

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

Discovery of a small molecule targeting ULK1-modulated cell death of triple negative breast cancer in vitro and in vivo

(2017) Lan Zhang et al.   Chemical Science

Assessing the performance of docking scoring function, FEP, MM-GBSA, and QM/MM-GBSA approaches on a series of PLK1 inhibitors

(2017) Chunlan Pu et al.   MedChemComm

Heat shock protein 90 and serine/threonine kinase B-Raf inhibitors have overlapping chemical space

(2017) A. Anighoro et al.   RSC Advances

Recent advances in dynamic docking for drug discovery

(2017) Marco De Vivo et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Using reverse docking to identify potential targets for ginsenosides

(2017) Kichul Park et al.   Journal of Ginseng Research

On the Integration of In Silico Drug Design Methods for Drug Repurposing

(2017) Eric March-Vila et al.   Frontiers in Pharmacology

The scoring bias in reverse docking and the score normalization strategy to improve success rate of target fishing

(2017) Qiyao Luo et al.   PLoS One

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

(2017) Max K. Leong et al.   Scientific Reports

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

In silico prediction of drug-target interaction networks based on drug chemical structure and protein sequences

(2017) Zhengwei Li et al.   Scientific Reports

Current trends in protein crystallization

(2016) José A. Gavira   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform

(2016) Gaurav Chopra et al.   CURRENT PHARMACEUTICAL DESIGN

Polypharmacology in Drug Discovery: A Review from Systems Pharmacology Perspective

(2016) Wenjuan Zhang et al.   CURRENT PHARMACEUTICAL DESIGN

Using reverse docking for target identification and its applications for drug discovery

(2016) Aeri Lee et al.   Expert Opinion on Drug Discovery

Exploiting computationally derived out-of-the-box protein conformations for drug design

(2016) Fabiana Caporuscio et al.   Future Medicinal Chemistry

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

(2016) Andrew Anighoro et al.   Journal of Chemical Information and Modeling

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

(2016) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations

(2016) Anthony J. Clark et al.   Journal of Chemical Theory and Computation

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

(2016) Vladimiras Oleinikovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Association Between Tuberculosis and Parkinson Disease

(2016) Chih-Hao Shen et al.   MEDICINE

Progress in protein crystallography

(2016) Zbigniew Dauter et al.   PROTEIN AND PEPTIDE LETTERS

ACTP: A webserver for predicting potential targets and relevant pathways of autophagy-modulating compounds

(2016) Tao Xie et al.   Oncotarget

Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase

(2016) Maria Agnese Morando et al.   Scientific Reports

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

(2016) Pasquale Pisani et al.   PLoS One

DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome

(2016) Heng Luo et al.   Scientific Reports

Role of computer-aided drug design in modern drug discovery

(2015) Stephani Joy Y. Macalino et al.   ARCHIVES OF PHARMACAL RESEARCH

Updates on drug–target network; facilitating polypharmacology and data integration by growth of DrugBank database

(2015) Farnaz Barneh et al.   BRIEFINGS IN BIOINFORMATICS

Machine-learning approaches in drug discovery: methods and applications

(2015) Antonio Lavecchia   DRUG DISCOVERY TODAY

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

(2015) Francesca Spyrakis et al.   Journal of Chemical Information and Modeling

Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise

(2015) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases

(2015) Yilin Meng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

MTiOpenScreen: a web server for structure-based virtual screening

(2015) Céline M. Labbé et al.   NUCLEIC ACIDS RESEARCH

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Computational polypharmacology comes of age

(2015) Giulio Rastelli et al.   Frontiers in Pharmacology

CANDO and the infinite drug discovery frontier

(2014) Mark Minie et al.   DRUG DISCOVERY TODAY

An overview of FDA-approved new molecular entities: 1827–2013

(2014) Michael S. Kinch et al.   DRUG DISCOVERY TODAY

Reverse docking: a powerful tool for drug repositioning and drug rescue

(2014) Prashant S Kharkar et al.   Future Medicinal Chemistry

Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening

(2014) Fabio Broccatelli et al.   Journal of Chemical Information and Modeling

Dual Histamine H3R/Serotonin 5-HT4R Ligands with Antiamnesic Properties: Pharmacophore-Based Virtual Screening and Polypharmacology

(2014) Alban Lepailleur et al.   Journal of Chemical Information and Modeling

Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

(2014) C. Da et al.   Journal of Chemical Information and Modeling

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge

(2014) Alexander L. Perryman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Polypharmacology: Challenges and Opportunities in Drug Discovery

(2014) Andrew Anighoro et al.   JOURNAL OF MEDICINAL CHEMISTRY

Pharmacophore-Based Similarity Scoring for DOCK

(2014) Lingling Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines

(2014) Montiago X. LaBute et al.   PLoS One

Big Data Deep Learning: Challenges and Perspectives

(2014) Xue-Wen Chen et al.   IEEE Access

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

(2014) Marco D'Abramo et al.   Frontiers in Genetics

Microsecond molecular dynamics simulation of Aβ42 and identification of a novel dual inhibitor of Aβ42 aggregation and BACE1 activity

(2013) Yuan-yuan Wang et al.   ACTA PHARMACOLOGICA SINICA

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling

(2013) Corentin Herbert et al.   CANCER CELL

Computational Drug Repositioning: From Data to Therapeutics

(2013) M R Hurle et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Predicting Targeted Polypharmacology for Drug Repositioning and Multi- Target Drug Discovery

(2013) X. Liu et al.   CURRENT MEDICINAL CHEMISTRY

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

(2013) Li-Quan Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Addressing Selective Polypharmacology of Antipsychotic Drugs Targeting the Bioaminergic Receptors through Receptor Dynamic Conformational Ensembles

(2013) Balaji Selvam et al.   Journal of Chemical Information and Modeling

Docking Challenge: Protein Sampling and Molecular Docking Performance

(2013) Khaled M. Elokely et al.   Journal of Chemical Information and Modeling

Molecular Similarity in Medicinal Chemistry

(2013) Gerald Maggiora et al.   JOURNAL OF MEDICINAL CHEMISTRY

Emerging Topics in Structure-Based Virtual Screening

(2013) Giulio Rastelli   PHARMACEUTICAL RESEARCH

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target fishing and docking studies of the novel derivatives of aryl-aminopyridines with potential anticancer activity

(2012) Slavica Erić et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

Proteomic characterization of the possible molecular targets of pyrrolizidine alkaloid isoline-induced hepatotoxicity

(2012) Zai-yong Wang et al.   ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY

Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors

(2012) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting New Indications for Approved Drugs Using a Proteochemometric Method

(2012) Sivanesan Dakshanamurthy et al.   JOURNAL OF MEDICINAL CHEMISTRY

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach

(2012) Jui-Chih Wang et al.   NUCLEIC ACIDS RESEARCH

Ginsenosides as anticancer agents: In vitro and in vivo activities, structure–activity relationships, and molecular mechanisms of action

(2012) Subhasree Ashok Nag   Frontiers in Pharmacology

Advances and applications of binding affinity prediction methods in drug discovery

(2011) Marco Daniele Parenti et al.   BIOTECHNOLOGY ADVANCES

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Combined SVM-based and docking-based virtual screening for retrieving novel inhibitors of c-Met

(2011) Qing-Qing Xie et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Integrating structure-based and ligand-based approaches for computational drug design

(2011) Gregory L Wilson et al.   Future Medicinal Chemistry

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

(2011) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

Pocketome: an encyclopedia of small-molecule binding sites in 4D

(2011) Irina Kufareva et al.   NUCLEIC ACIDS RESEARCH

SwissDock, a protein-small molecule docking web service based on EADock DSS

(2011) A. Grosdidier et al.   NUCLEIC ACIDS RESEARCH

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

(2011) Heng Luo et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Optimization Methods for Virtual Screening on Novel Computational Architectures

(2010) Horacio Perez-Sanchez et al.   Current Computer-Aided Drug Design

Template-Based Protein Modeling: Recent Methodological Advances

(2010) Pankaj Daga et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Correction: Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements

(2010) Enrico Defranchi et al.   PLoS One

Recent advances in computer-aided drug design

(2009) C. M. Song et al.   BRIEFINGS IN BIOINFORMATICS

Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening

(2009) Giulio Rastelli et al.   Chemical Biology & Drug Design

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

(2009) Ajay N. Jain   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Automated Docking Screens: A Feasibility Study

(2009) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

(2009) Lun Yang et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

PDTD: a web-accessible protein database for drug target identification

(2008) Zhenting Gao et al.   BMC BIOINFORMATICS

Natural products in drug discovery

(2008) A HARVEY   DRUG DISCOVERY TODAY

A simple and fast algorithm for K-medoids clustering

(2008) Hae-Sang Park et al.   EXPERT SYSTEMS WITH APPLICATIONS

Protein−Ligand Docking against Non-Native Protein Conformers

(2008) Marcel L. Verdonk et al.   Journal of Chemical Information and Modeling

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

(2008) William L. Jorgensen et al.   Journal of Chemical Theory and Computation

Discovery of Multitarget Inhibitors by Combining Molecular Docking with Common Pharmacophore Matching

(2008) Dengguo Wei et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach

(2006) I.M. Kapetanovic   CHEMICO-BIOLOGICAL INTERACTIONS