An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications
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Title
An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications
Authors
Keywords
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Journal
MOLECULES
Volume 24, Issue 9, Pages 1693
Publisher
MDPI AG
Online
2019-04-30
DOI
10.3390/molecules24091693
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Note: Only part of the references are listed.- Advances in Biomaterials for Drug Delivery
- (2018) Owen S. Fenton et al. ADVANCED MATERIALS
- Transverse Detection of DNA in a MoS 2 Nanopore
- (2018) Michael Graf et al. BIOPHYSICAL JOURNAL
- Dynamics and self-assembly of bio-functionalized gold nanoparticles in solution: Reactive molecular dynamics simulations
- (2018) Susanna Monti et al. Nano Research
- Computational investigation on DNA sequencing using functionalized graphene nanopores
- (2018) You-sheng Yu et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Modular assembly of proteins on nanoparticles
- (2018) Wenwei Ma et al. Nature Communications
- Biomining of MoS2 with Peptide-based Smart Biomaterials
- (2018) Sibel Cetinel et al. Scientific Reports
- Molecular Dynamics Simulation for All
- (2018) Scott A. Hollingsworth et al. NEURON
- Nano based drug delivery systems: recent developments and future prospects
- (2018) Jayanta Kumar Patra et al. JOURNAL OF NANOBIOTECHNOLOGY
- Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
- (2017) Zoe Cournia et al. Journal of Chemical Information and Modeling
- Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study
- (2017) Henrik Keränen et al. Journal of Chemical Theory and Computation
- Quality by design (QbD) approach of pharmacogenomics in drug designing and formulation development for optimization of drug delivery systems
- (2017) Sumeet Gupta et al. JOURNAL OF CONTROLLED RELEASE
- Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry
- (2017) Billy J. Williams-Noonan et al. JOURNAL OF MEDICINAL CHEMISTRY
- Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore
- (2016) Swati Bhattacharya et al. ACS Nano
- Computer-aided discovery of anti-HIV agents
- (2016) William L. Jorgensen BIOORGANIC & MEDICINAL CHEMISTRY
- Simulations of inorganic–bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities
- (2016) Hendrik Heinz et al. CHEMICAL SOCIETY REVIEWS
- In silico methods to address polypharmacology: current status, applications and future perspectives
- (2016) Antonio Lavecchia et al. DRUG DISCOVERY TODAY
- Application of Free Energy Perturbation for the Design of BACE1 Inhibitors
- (2016) Myriam Ciordia et al. Journal of Chemical Information and Modeling
- Role of Molecular Dynamics and Related Methods in Drug Discovery
- (2016) Marco De Vivo et al. JOURNAL OF MEDICINAL CHEMISTRY
- A study on the interactions of amino acids with nitrogen doped graphene; docking, MD simulation, and QM/MM studies
- (2016) Rahim Ghadari PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
- (2016) Isseki Yu et al. eLife
- Adsorption of biomolecules and polymers on silicates, glasses, and oxides: mechanisms, predictions, and opportunities by molecular simulation
- (2016) Hendrik Heinz Current Opinion in Chemical Engineering
- The ReaxFF reactive force-field: development, applications and future directions
- (2016) Thomas P Senftle et al. npj Computational Materials
- Biotic–Abiotic Interactions: Factors that Influence Peptide–Graphene Interactions
- (2015) Steve S. Kim et al. ACS Applied Materials & Interfaces
- Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified by Free-Energy Perturbation (FEP)
- (2015) Frank Lovering et al. ChemMedChem
- Molecular dynamics simulations of large macromolecular complexes
- (2015) Juan R Perilla et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Molecular dynamics in drug design
- (2015) Hongtao Zhao et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Computation of the binding free energy of peptides to graphene in explicit water
- (2015) Corrinne M. Welch et al. JOURNAL OF CHEMICAL PHYSICS
- Adsorption Orientation and Binding Motifs of Lysozyme and Chymotrypsin on Amorphous Silica
- (2015) Nils Hildebrand et al. Journal of Physical Chemistry C
- 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
- (2015) Lingle Wang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
- (2015) Hu Qiu et al. NANO LETTERS
- PubChem Substance and Compound databases
- (2015) Sunghwan Kim et al. NUCLEIC ACIDS RESEARCH
- Pyrido[4,3-e][1,2,4]triazolo[4,3-a]pyrazines as Selective, Brain Penetrant Phosphodiesterase 2 (PDE2) Inhibitors
- (2015) Frederik J. R. Rombouts et al. ACS Medicinal Chemistry Letters
- Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides
- (2014) Michaël L. Cartron et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
- Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas aeruginosa
- (2014) Jamie Parkin et al. BIOPHYSICAL JOURNAL
- Prediction of Specific Biomolecule Adsorption on Silica Surfaces as a Function of pH and Particle Size
- (2014) Fateme S. Emami et al. CHEMISTRY OF MATERIALS
- Molecular Mechanism of Selective Binding of Peptides to Silicon Surface
- (2014) Sathish Kumar Ramakrishnan et al. Journal of Chemical Information and Modeling
- Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model
- (2014) Jing Huang et al. Journal of Physical Chemistry Letters
- Close encounters with DNA
- (2014) C Maffeo et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Molecular-Level Understanding of Protein Adsorption at the Interface between Water and a Strongly Interacting Uncharged Solid Surface
- (2014) Matthew J. Penna et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Adhesion of lactoferrin and bone morphogenetic protein-2 to a rutile surface: dependence on the surface hydrophobicity
- (2014) Tianyang Sun et al. Biomaterials Science
- Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
- (2013) Marc W. van der Kamp et al. BIOCHEMISTRY
- Molecular determinants of drug–receptor binding kinetics
- (2013) Albert C. Pan et al. DRUG DISCOVERY TODAY
- GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
- (2013) Louise B. Wright et al. Journal of Chemical Theory and Computation
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- (2013) Hendrik Heinz et al. LANGMUIR
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- (2013) Lingyan Ruan et al. NANO LETTERS
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- (2013) Gongpu Zhao et al. NATURE
- Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review
- (2012) Tiejun Cheng et al. AAPS Journal
- Docking of Ubiquitin to Gold Nanoparticles
- (2012) Giorgia Brancolini et al. ACS Nano
- Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence
- (2012) Swati Bhattacharya et al. ACS Nano
- Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study
- (2012) Andrew T. Guy et al. BIOPHYSICAL JOURNAL
- ZINC: A Free Tool to Discover Chemistry for Biology
- (2012) John J. Irwin et al. Journal of Chemical Information and Modeling
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- (2012) Zaixing Yang et al. JOURNAL OF CHEMICAL PHYSICS
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- (2012) Siddharth V. Patwardhan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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- (2012) David B. Wells et al. NANO LETTERS
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- (2012) Gerald M Cherf et al. NATURE BIOTECHNOLOGY
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- (2012) Sérgio Filipe Sousa et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Organic—inorganic hybrid solar cells: A comparative review
- (2012) Matthew Wright et al. SOLAR ENERGY MATERIALS AND SOLAR CELLS
- Theoretical study on key factors in DNA sequencing with graphene nanopores
- (2012) Lijun Liang et al. RSC Advances
- Mechanized Silica Nanoparticles: A New Frontier in Theranostic Nanomedicine
- (2011) Michael W. Ambrogio et al. ACCOUNTS OF CHEMICAL RESEARCH
- Computational Investigation of DNA Detection Using Graphene Nanopores
- (2011) Chaitanya Sathe et al. ACS Nano
- Molecular Dynamics Simulations of DNA within a Nanopore: Arginine−Phosphate Tethering and a Binding/Sliding Mechanism for Translocation
- (2011) Peter J. Bond et al. BIOCHEMISTRY
- Molecular dynamics simulations and drug discovery
- (2011) Jacob D Durrant et al. BMC BIOLOGY
- The golden age: gold nanoparticles for biomedicine
- (2011) Erik C. Dreaden et al. CHEMICAL SOCIETY REVIEWS
- Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents
- (2011) Mariela Bollini et al. JOURNAL OF MEDICINAL CHEMISTRY
- Efficient Discovery of Potent Anti-HIV Agents Targeting the Tyr181Cys Variant of HIV Reverse Transcriptase
- (2011) William L. Jorgensen et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Preferential Binding of Peptides to Graphene Edges and Planes
- (2011) Sang N. Kim et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Controlling molecular transport through nanopores
- (2011) U. F. Keyser Journal of the Royal Society Interface
- Ab initio derived force-field parameters for molecular dynamics simulations of deprotonated amorphous-SiO2/water interfaces
- (2011) Anke Butenuth et al. PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS
- Pathway and mechanism of drug binding to G-protein-coupled receptors
- (2011) Ron O. Dror et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Porous Polymer Monolithic Column with Surface-Bound Gold Nanoparticles for the Capture and Separation of Cysteine-Containing Peptides
- (2010) Yan Xu et al. ANALYTICAL CHEMISTRY
- The Role of Water Molecules in Computational Drug Design
- (2010) Stephanie de Beer et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- 3D-QSAR in Drug Design - A Review
- (2010) Jitender Verma et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Pharmacophore modeling and applications in drug discovery: challenges and recent advances
- (2010) Sheng-Yong Yang DRUG DISCOVERY TODAY
- A first principles based polarizable O(N) interatomic force field for bulk silica
- (2010) J. R. Kermode et al. JOURNAL OF CHEMICAL PHYSICS
- Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome
- (2010) Xiaoxia Ge et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Multifunctional Mesoporous Composite Microspheres with Well-Designed Nanostructure: A Highly Integrated Catalyst System
- (2010) Yonghui Deng et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Adsorption Mechanism of Ribosomal Protein L2 onto a Silica Surface: A Molecular Dynamics Simulation Study
- (2010) Ryo Tosaka et al. LANGMUIR
- DNA Translocation through Graphene Nanopores
- (2010) Christopher A. Merchant et al. NANO LETTERS
- DNA Translocation through Graphene Nanopores
- (2010) Grégory F. Schneider et al. NANO LETTERS
- Graphene as a subnanometre trans-electrode membrane
- (2010) S. Garaj et al. NATURE
- Nanotechnology: Holes with an edge
- (2010) Hagan Bayley NATURE
- Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores
- (2010) Adam R. Hall et al. Nature Nanotechnology
- Nanopore DNA sequencing with MspA
- (2010) I. M. Derrington et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Atomic-Level Characterization of the Structural Dynamics of Proteins
- (2010) D. E. Shaw et al. SCIENCE
- Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding
- (2009) Peter L. Freddolino et al. BIOPHYSICAL JOURNAL
- Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study
- (2009) Mareike Zink et al. BIOPHYSICAL JOURNAL
- Long-timescale molecular dynamics simulations of protein structure and function
- (2009) John L Klepeis et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Affinity Scale for the Interaction of Amino Acids with Silica Surfaces
- (2009) Albert Rimola et al. Journal of Physical Chemistry C
- Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd−Au Bimetal Surfaces in Aqueous Solution
- (2009) Hendrik Heinz et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Well-Dispersed Fractal Aggregates as Filler in Polymer−Silica Nanocomposites: Long-Range Effects in Rheology
- (2009) Nicolas Jouault et al. MACROMOLECULES
- Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
- (2009) E. Villa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains
- (2009) Ying Yin et al. STRUCTURE
- Interaction of biomolecular systems with titanium-based materials: computational investigations
- (2009) Vincenzo Carravetta et al. THEORETICAL CHEMISTRY ACCOUNTS
- Noble Metals on the Nanoscale: Optical and Photothermal Properties and Some Applications in Imaging, Sensing, Biology, and Medicine
- (2008) Prashant K. Jain et al. ACCOUNTS OF CHEMICAL RESEARCH
- Optical Resonance-Enhanced Absorption-Based Near-Field Immunochip Biosensor for Allergen Detection
- (2008) Irene Maier et al. ANALYTICAL CHEMISTRY
- DNA Translocation Governed by Interactions with Solid-State Nanopores
- (2008) Meni Wanunu et al. BIOPHYSICAL JOURNAL
- Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain
- (2008) Peter L. Freddolino et al. BIOPHYSICAL JOURNAL
- FFSiOH: a New Force Field for Silica Polymorphs and Their Hydroxylated Surfaces Based on Periodic B3LYP Calculations
- (2008) Alfonso Pedone et al. CHEMISTRY OF MATERIALS
- Investigating Alanine–Silica Interaction by Means of First-Principles Molecular-Dynamics Simulations
- (2008) Marco Nonella et al. CHEMPHYSCHEM
- Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
- (2008) F. Iori et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation
- (2008) Kimberly Chenoweth et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Peptide/TiO2Surface Interaction: A Theoretical and Experimental Study on the Structure of Adsorbed ALA-GLU and ALA-LYS
- (2008) S. Monti et al. LANGMUIR
- Electromechanical Unzipping of Individual DNA Molecules Using Synthetic Sub-2 nm Pores
- (2008) Ben McNally et al. NANO LETTERS
- Stretching and unzipping nucleic acid hairpins using a synthetic nanopore
- (2008) Q. Zhao et al. NUCLEIC ACIDS RESEARCH
- Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
- (2008) M. L. Klein et al. SCIENCE
- Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase
- (2008) Anil K. Agarwal et al. TETRAHEDRON
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