Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
出版年份 2018 全文链接
标题
Multiscale methods in drug design bridge chemical and biological
complexity in the search for cures
作者
关键词
-
出版物
Nature Reviews Chemistry
Volume 2, Issue 4, Pages 0148
出版商
Springer Nature
发表日期
2018-04-11
DOI
10.1038/s41570-018-0148
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Drug target residence time: a misleading concept
- (2018) Rutger H.A. Folmer DRUG DISCOVERY TODAY
- L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib
- (2018) D. Callegari et al. Chemical Science
- Multiscale analysis of enantioselectivity in enzyme-catalysed ‘lethal synthesis’ using projector-based embedding
- (2018) Xinglong Zhang et al. Royal Society Open Science
- PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories
- (2017) James A. Graham et al. Journal of Chemical Information and Modeling
- Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8
- (2017) Donatella Callegari et al. Journal of Chemical Information and Modeling
- A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures
- (2017) Lorenzo Boninsegna et al. Journal of Chemical Theory and Computation
- Systematic Quantum Mechanical Region Determination in QM/MM Simulation
- (2017) Maria Karelina et al. Journal of Chemical Theory and Computation
- D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
- (2017) Zied Gaieb et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding
- (2017) Lane W. Votapka et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
- (2017) Tyler M. Earnest et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
- (2017) Nuria Plattner et al. Nature Chemistry
- ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
- (2017) Horng D. Ou et al. SCIENCE
- ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost
- (2017) J. S. Smith et al. Chemical Science
- Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations
- (2017) Juan R. Perilla et al. Nature Communications
- Building bridges between cellular and molecular structural biology
- (2017) Ardan Patwardhan et al. eLife
- Low Data Drug Discovery with One-Shot Learning
- (2017) Han Altae-Tran et al. ACS Central Science
- Inhibition of prenylated KRAS in a lipid environment
- (2017) Johanna M. Jansen et al. PLoS One
- Living on the edge: Simulations of bacterial outer-membrane proteins
- (2016) Anna Pavlova et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
- (2016) Ulf Ryde et al. CHEMICAL REVIEWS
- Coarse-Grained Protein Models and Their Applications
- (2016) Sebastian Kmiecik et al. CHEMICAL REVIEWS
- Multi-class and multi-scale models of complex biological phenomena
- (2016) Jessica S Yu et al. CURRENT OPINION IN BIOTECHNOLOGY
- Multiscale simulation of DNA
- (2016) Pablo D Dans et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations
- (2016) Jonathan D. Tyzack et al. Journal of Chemical Information and Modeling
- Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
- (2016) Christopher T. Lee et al. Journal of Chemical Information and Modeling
- Perspective: Quantum mechanical methods in biochemistry and biophysics
- (2016) Qiang Cui JOURNAL OF CHEMICAL PHYSICS
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules
- (2016) Jeffrey Skolnick JOURNAL OF CHEMICAL PHYSICS
- A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase
- (2016) Simon J. Bennie et al. Journal of Chemical Theory and Computation
- Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam
- (2016) J. Rydzewski et al. Journal of Chemical Theory and Computation
- D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
- (2016) Symon Gathiaka et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength
- (2016) Elena Segala et al. JOURNAL OF MEDICINAL CHEMISTRY
- Role of Molecular Dynamics and Related Methods in Drug Discovery
- (2016) Marco De Vivo et al. JOURNAL OF MEDICINAL CHEMISTRY
- Two Relations to Estimate Membrane Permeability Using Milestoning
- (2016) Lane W. Votapka et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling
- (2016) Callum J. Dickson et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Design of a hyperstable 60-subunit protein icosahedron
- (2016) Yang Hsia et al. NATURE
- A comprehensive map of molecular drug targets
- (2016) Rita Santos et al. NATURE REVIEWS DRUG DISCOVERY
- Full-length p53 tetramer bound to DNA and its quaternary dynamics
- (2016) Ö Demir et al. ONCOGENE
- Multiscale simulation of molecular processes in cellular environments
- (2016) Mara Chiricotto et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
- Enzyme catalysis by entropy without Circe effect
- (2016) Masoud Kazemi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization
- (2016) Jordan R. Willis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transition path theory analysis of c-Src kinase activation
- (2016) Yilin Meng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Visualizing the molecular sociology at the HeLa cell nuclear periphery
- (2016) J. Mahamid et al. SCIENCE
- Accurate design of megadalton-scale two-component icosahedral protein complexes
- (2016) J. B. Bale et al. SCIENCE
- A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
- (2016) Nathan Mih et al. PLoS Computational Biology
- ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units
- (2015) Johann Biedermann et al. BIOPHYSICAL JOURNAL
- Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes
- (2015) Jamie Parkin et al. BIOPHYSICAL JOURNAL
- Membrane protein structural biology using X-ray free electron lasers
- (2015) Richard Neutze et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules
- (2015) Matteo Levantino et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method
- (2015) Gerhard König et al. Journal of Chemical Theory and Computation
- Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems
- (2015) Pandian Sokkar et al. Journal of Chemical Theory and Computation
- The adaptive buffered force QM/MM method in the CP2K and AMBER software packages
- (2015) Letif Mones et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- 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
- Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
- (2015) Pratyush Tiwary et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates
- (2015) Varnavas D. Mouchlis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
- (2015) Nuria Plattner et al. Nature Communications
- Allostery through the computational microscope: cAMP activation of a canonical signalling domain
- (2015) Robert D. Malmstrom et al. Nature Communications
- Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
- (2015) Luca Mollica et al. Scientific Reports
- Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study
- (2015) Nils A. Berglund et al. PLoS Computational Biology
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
- (2015) Lane W. Votapka et al. PLoS Computational Biology
- In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
- (2015) Alan Gray et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Bridging scales through multiscale modeling: a case study on protein kinase A
- (2015) Britton W. Boras et al. Frontiers in Physiology
- Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms
- (2014) Andrea Cavalli et al. ACCOUNTS OF CHEMICAL RESEARCH
- QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases
- (2014) Ewa I. Chudyk et al. CHEMICAL COMMUNICATIONS
- Finding the right fit: chiseling structures out of cryo-electron microscopy maps
- (2014) Elizabeth Villa et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Computational modeling of subcellular transport and signaling
- (2014) Johan Hake et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Cellular and molecular structure as a unifying framework for whole-cell modeling
- (2014) Elijah Roberts CURRENT OPINION IN STRUCTURAL BIOLOGY
- Accurate and systematically improvable density functional theory embedding for correlated wavefunctions
- (2014) Jason D. Goodpaster et al. JOURNAL OF CHEMICAL PHYSICS
- Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
- (2014) Samuel Genheden et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4
- (2014) Gerhard König et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein–Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase
- (2014) Christopher J. Woods et al. JOURNAL OF PHYSICAL CHEMISTRY B
- cellPACK: a virtual mesoscope to model and visualize structural systems biology
- (2014) Graham T Johnson et al. NATURE METHODS
- Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase
- (2014) C. M. Casadei et al. SCIENCE
- Diffuse X-Ray Scattering to Model Protein Motions
- (2014) Michael E. Wall et al. STRUCTURE
- A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase
- (2014) Kara E. Ranaghan et al. Chemical Science
- A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
- (2014) Richard Lonsdale et al. PLoS Computational Biology
- LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
- (2014) Jacob D. Durrant et al. PLoS Computational Biology
- Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine
- (2013) David E. Shaw BIOPHYSICAL JOURNAL
- Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography
- (2013) Elizabeth Villa et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Accurate basis set truncation for wavefunction embedding
- (2013) Taylor A. Barnes et al. JOURNAL OF CHEMICAL PHYSICS
- Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
- (2013) Manuel Doemer et al. Journal of Chemical Theory and Computation
- The Theory of Ultra-Coarse-Graining. 1. General Principles
- (2013) James F. Dama et al. Journal of Chemical Theory and Computation
- A stochastic finite element model for the dynamics of globular macromolecules
- (2013) Robin C. Oliver et al. JOURNAL OF COMPUTATIONAL PHYSICS
- Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9
- (2013) Richard Lonsdale et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
- (2013) Gongpu Zhao et al. NATURE
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
- (2013) Kai J. Kohlhoff et al. Nature Chemistry
- Photodynamic therapy for photochemists
- (2013) S. G. Bown PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
- Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables
- (2013) J. Juraszek et al. PHYSICAL REVIEW LETTERS
- Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function
- (2013) H. J. Hocker et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Inteins: nature's gift to protein chemists
- (2013) Neel H. Shah et al. Chemical Science
- Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
- (2013) Christopher D. Wassman et al. Nature Communications
- A Coarse-Grained Protein Model in a Water-like Solvent
- (2013) Sumit Sharma et al. Scientific Reports
- Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity
- (2013) Christopher J. Woods et al. Scientific Reports
- Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?
- (2012) Robert V. Swift et al. Chemical Biology & Drug Design
- Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation
- (2012) Elijah Roberts et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Unassisted Transport of N-Acetyl-l-tryptophanamide through Membrane: Experiment and Simulation of Kinetics
- (2012) Alfredo E. Cardenas et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Ab Initio Quantum Chemistry for Protein Structures
- (2012) Heather J. Kulik et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies
- (2012) Daniel Russel et al. PLOS BIOLOGY
- Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations
- (2011) Weihua Zheng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The resurgence of covalent drugs
- (2011) Juswinder Singh et al. NATURE REVIEWS DRUG DISCOVERY
- Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
- (2011) S. J. Fleishman et al. SCIENCE
- The empirical valence bond model: theory and applications
- (2011) Shina C. L. Kamerlin et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Hydrogen exchange mass spectrometry for studying protein structure and dynamics
- (2010) Lars Konermann et al. CHEMICAL SOCIETY REVIEWS
- Imaging cellular architecture with X-rays
- (2010) Carolyn A Larabell et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes
- (2010) M. Orsi et al. Journal of the Royal Society Interface
- Targeted Enzyme Prodrug Therapies
- (2010) N. Schellmann et al. MINI-REVIEWS IN MEDICINAL CHEMISTRY
- Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
- (2010) Sean R. McGuffee et al. PLoS Computational Biology
- Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
- (2009) Ming-Hsun Ho et al. Journal of Chemical Theory and Computation
- Discovery Through the Computational Microscope
- (2009) Eric H. Lee et al. STRUCTURE
- Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
- (2008) Rex A. Kerr et al. SIAM JOURNAL ON SCIENTIFIC COMPUTING
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