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Computational Predictions for Multi-Target Drug Design

https://doi.org/10.1007/7653_2018_26

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Identification of Potential Multitarget Antimalarial Drugs

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Computational Multitarget Drug Discovery

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Scalable molecular dynamics with NAMD

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VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers

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Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

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Challenges and advances in computational docking: 2009 in review

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QSAR Modelling of Rat Acute Toxicity on the Basis of PASS Prediction

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AutoWeka: Toward an Automated Data Mining Software for QSAR and QSPR Studies

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An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

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DNA minor groove binding of small molecules: Experimental and computational evidence

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COMT-inhibition increases serum levels of dihydroxyphenylacetic acid (DOPAC) in patients with advanced Parkinson's disease

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GROMACS: A message-passing parallel molecular dynamics implementation

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The Increasing Role of QM/MM in Drug Discovery

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Selected Statistical Methods in QSAR

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Unified QSAR approach to antimicrobials. Part 3: First multi-tasking QSAR model for Input-Coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds

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Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug–drug complex networks

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Multi-target spectral moment QSAR versus ANN for antiparasitic drugs against different parasite species

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Unified Markov thermodynamics based on stochastic forms to classify drugs considering molecular structure, partition system, and biological species:

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Data flow modeling, data mining and QSAR in high-throughput discovery of functional nanomaterials

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In silico repositioning of approved drugs for rare and neglected diseases

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CANDO and the infinite drug discovery frontier

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Binding of DNA with Rhodamine B: Spectroscopic and molecular modeling studies

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Using the TOPS-MODE approach to fit multi-target QSAR models for tyrosine kinases inhibitors

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Molecular dynamics in drug design

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Evaluation of various inverse docking schemes in multiple targets identification

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Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets

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Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies

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Can we rationally design promiscuous drugs?

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High-throughput identification of off-targets for the mechanistic study of severe adverse drug reactions induced by analgesics

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Novel paradigms for drug discovery: computational multitarget screening

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The Hallmarks of Cancer

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University of California, San Francisco

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Desirability-Based Methods of Multiobjective Optimization and Ranking for Global QSAR Studies. Filtering Safe and Potent Drug Candidates from Combinatorial Libraries

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QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?

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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

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A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔTm

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QSAR Modeling: Where Have You Been? Where Are You Going To?

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Polypharmacology: Challenges and Opportunities in Drug Discovery

inferredcites →https://doi.org/10.1021/jp509326ropenalex-snapshot

Thermodynamic Study of Rhodamine 123-Calf Thymus DNA Interaction: Determination of Calorimetric Enthalpy by Optical Melting Study

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The GROMOS Biomolecular Simulation Program Package

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Alignment-Free Prediction of a Drug−Target Complex Network Based on Parameters of Drug Connectivity and Protein Sequence of Receptors

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Escape from HER-family tyrosine kinase inhibitor therapy by the kinase-inactive HER3

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Mechanisms of Disease: understanding resistance to HER2-targeted therapy in human breast cancer

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RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloidcoralyne

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Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei

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Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach

inferredcites →https://doi.org/10.1080/10629360701843649openalex-snapshot

Computer-aided prediction for medicinal chemistry via the Internet

inferredcites →https://doi.org/10.1093/bib/bbr006openalex-snapshot

Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases

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Physical Chemistry for the Life Sciences

inferredcites →https://doi.org/10.1093/nar/gkq400openalex-snapshot

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

inferredcites →https://doi.org/10.1103/physrev.159.98openalex-snapshot

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

inferredcites →https://doi.org/10.1126/science.1056072openalex-snapshot

Principles for the Buffering of Genetic Variation

inferredcites →https://doi.org/10.1146/annurev.biophys.28.1.155openalex-snapshot

MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects

inferredcites →https://doi.org/10.1158/1541-7786.mcr-06-0404openalex-snapshot

The Role of VEGF and EGFR Inhibition: Implications for Combining Anti–VEGF and Anti–EGFR Agents

inferredcites →https://doi.org/10.1177/1934578x1200700308openalex-snapshot

DNA Binding Studies of Vinca Alkaloids: Experimental and Computational Evidence

inferredcites →https://doi.org/10.1186/1758-2946-5-33openalex-snapshot

Inferring multi-target QSAR models with taxonomy-based multi-task learning

inferredcites →https://doi.org/10.1371/journal.pcbi.1002503openalex-snapshot

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

inferredcites →https://doi.org/10.1371/journal.pone.0011955openalex-snapshot

Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina

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Sequence Specific Binding of Beta Carboline Alkaloid Harmalol with Deoxyribonucleotides: Binding Heterogeneity, Conformational, Thermodynamic and Cytotoxic Aspects

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Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

inferredcites →https://doi.org/10.1517/17460441.2015.1006195openalex-snapshot

Multitasking models for quantitative structure–biological effect relationships: current status and future perspectives to speed up drug discovery

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inferredcites →https://doi.org/10.2174/092986607781483831openalex-snapshot

ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes

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

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Advanced In Silico Approaches for Drug Discovery: Mining Information from Multiple Biological and Chemical Data Through mtk- QSBER and pt-QSPR Strategies

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Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform

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Recent Advances in the Development of Multi-Kinase Inhibitors

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A Comparison of Physicochemical Property Profiles of Marketed Oral Drugs and Orally Bioavailable Anti-Cancer Protein Kinase Inhibitors in Clinical Development

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Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation

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A comparison on the biochemical activities of Fluorescein disodium, Rose Bengal and Rhodamine 101 in the light of DNA binding, antimicrobial and cytotoxic study

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