Use of Integrated Computational Approaches in the Search for New Therapeutic Agents

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Molecular Informatics

• Publication date

  2016-09-01

• Fields of study

  Chemistry, Medicine, Computer Science

• Identifiers
  DOI 10.1002/minf.201501028PMID 27546035
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A Real-World Perspective on Molecular Design.

  2016cited by this paper
• Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening

  2016cited by this paper
• Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

  2016cited by this paper
• Perspective: Polarizable continuum models for quantum-mechanical descriptions.

  2016cited by this paper
• Large-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4

  2015cited by this paper
• Cationic porphyrins are tunable gatekeepers of the 20S proteasome† †Electronic supplementary information (ESI) available: It is reporting computational details, semi-log plots of residual CP activities, Molprobity results. See DOI: 10.1039/c5sc03312h

  2015cited by this paper
• Marine inspired antiplasmodial thiazinoquinones: synthesis, computational studies and electrochemical assays

  2015cited by this paper
• Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.

  2015cited by this paper
• How the flexibility of human histone deacetylases influences ligand binding: an overview.

  2015cited by this paper
• The revolution will not be crystallized: a new method sweeps through structural biology

  2015cited by this paper
• Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.

  2015cited by this paper
• Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

  2015cited by this paper
• From Protein Communication to Drug Discovery.

  2015cited by this paper
• Haem-activated promiscuous targeting of artemisinin in Plasmodium falciparum

  2015cited by this paper
• Enhanced sampling techniques in molecular dynamics simulations of biological systems.

  2015cited by this paper
• Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review

  2015cited by this paper
• New antimalarial 3-methoxy-1,2-dioxanes: optimization of cellular pharmacokinetics and pharmacodynamics properties by incorporation of amino and N-heterocyclic moieties at C4

  2015cited by this paper
• GTP is an allosteric modulator of the interaction between the guanylate-binding protein 1 and the prosurvival kinase PIM1.

  2015cited by this paper
• Orienting the heterocyclic periphery: a structural model for chloroquine's antimalarial activity.

  2014cited by this paper
• Endoperoxide polyketides from a Chinese Plakortis simplex: further evidence of the impact of stereochemistry on antimalarial activity of simple 1,2-dioxanes.

  2014cited by this paper
• Computational Methods in Drug Discovery

  2014cited by this paper
• Identification of the First Inhibitor of the GBP1:PIM1 Interaction. Implications for the Development of a New Class of Anticancer Agents against Paclitaxel Resistant Cancer Cells

  2014cited by this paper
• Current and emerging opportunities for molecular simulations in structure-based drug design

  2014cited by this paper
• Ensemble-Based Docking Using Biased Molecular Dynamics

  2014cited by this paper
• Optimized Synthesis and Antimalarial Activity of 1,2‐Dioxane‐4‐carboxamides

  2014cited by this paper
• Impact of computational structure-based methods on drug discovery.

  2014cited by this paper
• Influence of host iron status on Plasmodium falciparum infection

  2014cited by this paper
• Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

  2014cited by this paper
• New anticancer agents mimicking protein recognition motifs.

  2013cited by this paper
• Learning To Fold Proteins Using Energy Landscape Theory.

  2013cited by this paper
• One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade.

  2013cited by this paper
• Targeting the redox metabolism of Plasmodium falciparum.

  2013cited by this paper
• Further optimization of plakortin pharmacophore: structurally simple 4-oxymethyl-1,2-dioxanes with promising antimalarial activity.

  2013cited by this paper
• Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions.

  2013cited by this paper
• The eukaryotic linear motif resource ELM: 10 years and counting

  2013cited by this paper
• The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces

  2013cited by this paper
• Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

  2012cited by this paper
• Tetramerization of human guanylate‐binding protein 1 is mediated by coiled‐coil formation of the C‐terminal α‐helices

  2012cited by this paper
• Probing the diverse landscape of protein flexibility and binding.

  2012cited by this paper
• Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

  2012cited by this paper
• A physico-biochemical study on potential redox-cyclers as antimalarial and anti-schistosomal drugs.

  2012cited by this paper
• Tubulins as therapeutic targets in cancer: from bench to bedside.

  2012cited by this paper
• Redox regulation in malaria: current concepts and pharmacotherapeutic implications.

  2012cited by this paper
• Class III β‐tubulin and the cytoskeletal gateway for drug resistance in ovarian cancer

  2012cited by this paper
• GSAFold: A new application of GSA to protein structure prediction

  2012cited by this paper
• A new class of antimalarial dioxanes obtained through a simple two-step synthetic approach: rational design and structure-activity relationship studies.

  2011cited by this paper
• Class III β-tubulin (TUBB3): more than a biomarker in solid tumors?

  2011cited by this paper
• Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation.

  2011cited by this paper
• Investigation of the Bcl-2 multimerisation process: structural and functional implications.

  2011cited by this paper
• Software and resources for computational medicinal chemistry.

  2011cited by this paper
• Toxicokinetic and toxicodynamic (TK/TD) evaluation to determine and predict the neurotoxicity of artemisinins.

  2011cited by this paper
• Antimalarials based on the dioxane scaffold of plakortin. A concise synthesis and SAR studies.

  2011cited by this paper
• Integrating structure-based and ligand-based approaches for computational drug design.

  2011cited by this paper
• PubChem's BioAssay Database

  2011cited by this paper
• Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor

  2011cited by this paper
• Successful applications of computer aided drug discovery: moving drugs from concept to the clinic.

  2010cited by this paper
• Challenges in protein folding simulations: Timescale, representation, and analysis.

  2010cited by this paper
• Manadoperoxides A-D from the Indonesian sponge Plakortis cfr. simplex. Further insights on the structure-activity relationships of simple 1,2-dioxane antimalarials.

  2010cited by this paper
• Mechanism of GTPase-activity-induced self-assembly of human guanylate binding protein 1.

  2010cited by this paper
• Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

  2010cited by this paper
• Artemisinin resistance: current status and scenarios for containment

  2010cited by this paper
• Artemisinin resistance: current status and scenarios for containment

  2010cited by this paper
• Insight into the mechanism of action of plakortins, simple 1,2-dioxane antimalarials.

  2010cited by this paper
• Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors.

  2009cited by this paper
• Redox-Directed Cancer Therapeutics: Molecular Mechanisms and Opportunities

  2009cited by this paper
• Role of individual domains and identification of internal gap in human guanylate binding protein-1.

  2009cited by this paper
• Nucleotide dependent cysteine reactivity of hGBP1 uncovers a domain movement during GTP hydrolysis

  2009cited by this paper
• Long-timescale molecular dynamics simulations of protein structure and function.

  2009cited by this paper
• Paclitaxel directly binds to Bcl-2 and functionally mimics activity of Nur77.

  2009cited by this paper
• Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.

  2009cited by this paper
• Hypoxia induces class III beta-tubulin gene expression by HIF-1alpha binding to its 3' flanking region.

  2008cited by this paper
• Statistically optimal analysis of samples from multiple equilibrium states.

  2008cited by this paper
• Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

  2008cited by this paper
• PROMALS3D: a tool for multiple protein sequence and structure alignments

  2008cited by this paper
• Is class III beta-tubulin a predictive factor in patients receiving tubulin-binding agents?

  2008cited by this paper
• Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis

  2008cited by this paper
• Exploiting protein fluctuations at the active-site gorge of human cholinesterases: further optimization of the design strategy to develop extremely potent inhibitors.

  2008cited by this paper
• Flexible protein–flexible ligand docking with disrupted velocity simulated annealing

  2008cited by this paper
• Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking

  2008cited by this paper
• How Do Proteins Interact?

  2008cited by this paper
• A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules

  2007cited by this paper
• Conformational Sampling of Bioactive Molecules: A Comparative Study

  2007cited by this paper
• Looking at drug resistance mechanisms for microtubule interacting drugs: does TUBB3 work?

  2007cited by this paper
• New developments in synthetic peroxidic drugs as artemisinin mimics.

  2007cited by this paper
• MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

  2007cited by this paper
• Production of the antimalarial drug precursor artemisinic acid in engineered yeast

  2006cited by this paper
• Endoperoxide derivatives from marine organisms: 1,2-dioxanes of the plakortin family as novel antimalarial agents.

  2006cited by this paper
• Understanding ensemble protein folding at atomic detail

  2006cited by this paper
• New Tools Provide New Insights in NMR Studies of Protein Dynamics

  2006cited by this paper
• How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP

  2006cited by this paper
• Antimalarial Polyketide Cycloperoxides from the Marine SpongePlakortis simplex

  2005cited by this paper
• Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

  2005cited by this paper
• Molecular mechanisms of resistance in antimalarial chemotherapy: the unmet challenge.

  2005cited by this paper
• Linear motifs: Evolutionary interaction switches

  2005cited by this paper
• Newly developed basis sets for density functional calculations

  2005cited by this paper
• The dynamin superfamily: universal membrane tubulation and fission molecules?

  2004cited by this paper
• Hydroxyl radical scavenging and singlet oxygen quenching properties of polyamines

  2004cited by this paper
• Synthetic peroxides as antimalarials

  2004cited by this paper
• Achieving linear-scaling computational cost for the polarizable continuum model of solvation

  2004cited by this paper
• New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution

  2002cited by this paper

• Artificial Intelligence in the repurposing of potential herbs for filariasis therapy

  2024cites this paper
• Mapping of Protein Binding Sites using clustering algorithms - Development of a pharmacophore based drug discovery tool.

  2022cites this paper
• Identification of Potential Inhibitors of Cathepsin‐B using Shape & Pharmacophore‐based Virtual Screening, Molecular Docking and Explicit Water Thermodynamics

  2020cites this paper
• Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States

  2020cites this paper
• New insights into the mechanistic action of methyldehydrodieugenol B towards Leishmania (L.) infantum via a multiplatform based untargeted metabolomics approach

  2017cites this paper
• Drug Treatments for Core Symptoms of Autism Spectrum Disorder: Unmet Needs and Future Directions

  2017cites this paper
• Electrostatic Map Of Proteasome α-Rings Encodes The Design of Allosteric Porphyrin-Based Inhibitors Able To Affect 20S Conformation By Cooperative Binding

  2017cites this paper