Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
出版年份 2017 全文链接
标题
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
作者
关键词
-
出版物
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume 8, Issue 1, Pages e1343
出版商
Wiley
发表日期
2017-10-06
DOI
10.1002/wcms.1343
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems
- (2017) Luming Meng et al. JOURNAL OF CHEMICAL PHYSICS
- Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding
- (2017) Brooke E. Husic et al. Journal of Chemical Theory and Computation
- Kinetics-Controlled Amphiphile Self-Assembly Processes
- (2017) Xiaoyan Zheng et al. Journal of Physical Chemistry Letters
- Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
- (2017) Nuria Plattner et al. Nature Chemistry
- Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models
- (2016) Lu Zhang et al. ACCOUNTS OF CHEMICAL RESEARCH
- Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
- (2016) Jeffrey R. Wagner et al. CHEMICAL REVIEWS
- Dimensional reduction of Markov state models from renormalization group theory
- (2016) S. Orioli et al. JOURNAL OF CHEMICAL PHYSICS
- Density-based cluster algorithms for the identification of core sets
- (2016) Oliver Lemke et al. JOURNAL OF CHEMICAL PHYSICS
- Optimized parameter selection reveals trends in Markov state models for protein folding
- (2016) Brooke E. Husic et al. JOURNAL OF CHEMICAL PHYSICS
- Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems
- (2016) Guillermo Pérez-Hernández et al. Journal of Chemical Theory and Computation
- Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins
- (2016) Florian Sittel et al. Journal of Chemical Theory and Computation
- HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
- (2016) S. Doerr et al. Journal of Chemical Theory and Computation
- Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories
- (2016) Song Liu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit
- (2016) Bin W. Zhang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models
- (2016) Lizhe Zhu et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Multiensemble Markov models of molecular thermodynamics and kinetics
- (2016) Hao Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue
- (2016) Lin-Tai Da et al. Nature Communications
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
- (2016) Tatiana Maximova et al. PLoS Computational Biology
- Markov State Models Provide Insights into Dynamic Modulation of Protein Function
- (2015) Diwakar Shukla et al. ACCOUNTS OF CHEMICAL RESEARCH
- A critical appraisal of Markov state models
- (2015) Ch. Schütte et al. European Physical Journal-Special Topics
- Exact milestoning
- (2015) Juan M. Bello-Rivas et al. JOURNAL OF CHEMICAL PHYSICS
- Contact- and distance-based principal component analysis of protein dynamics
- (2015) Matthias Ernst et al. JOURNAL OF CHEMICAL PHYSICS
- Variational cross-validation of slow dynamical modes in molecular kinetics
- (2015) Robert T. McGibbon et al. JOURNAL OF CHEMICAL PHYSICS
- Modeling Molecular Kinetics with tICA and the Kernel Trick
- (2015) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation
- (2015) Frank Noé et al. Journal of Chemical Theory and Computation
- Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps
- (2015) Lorenzo Boninsegna et al. Journal of Chemical Theory and Computation
- FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs
- (2015) Maxwell I. Zimmerman et al. Journal of Chemical Theory and Computation
- PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
- (2015) Martin K. Scherer et al. Journal of Chemical Theory and Computation
- Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity
- (2015) Eva Nogales et al. MOLECULAR CELL
- Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
- (2015) Gregory R. Bowman et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A network of molecular switches controls the activation of the two-component response regulator NtrC
- (2015) Dan K. Vanatta et al. Nature Communications
- Allostery through the computational microscope: cAMP activation of a canonical signalling domain
- (2015) Robert D. Malmstrom et al. Nature Communications
- Cloud computing approaches for prediction of ligand binding poses and pathways
- (2015) Morgan Lawrenz et al. Scientific Reports
- Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
- (2015) Lu Zhang et al. PLoS Computational Biology
- Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
- (2015) Hanlun Jiang et al. PLoS Computational Biology
- A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
- (2015) Lin-Tai Da et al. PLoS Computational Biology
- Markov state models of biomolecular conformational dynamics
- (2014) John D Chodera et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Perspective: Markov models for long-timescale biomolecular dynamics
- (2014) C. R. Schwantes et al. JOURNAL OF CHEMICAL PHYSICS
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
- (2014) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems
- (2014) Fu Kit Sheong et al. Journal of Chemical Theory and Computation
- Variational Approach to Molecular Kinetics
- (2014) Feliks Nüske et al. Journal of Chemical Theory and Computation
- Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models
- (2014) Vincent A. Voelz et al. Journal of Chemical Theory and Computation
- Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models
- (2014) Gerhard Hummer et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Millisecond dynamics of RNA polymerase II translocation at atomic resolution
- (2014) D.-A. Silva et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Activation pathway of Src kinase reveals intermediate states as targets for drug design
- (2014) Diwakar Shukla et al. Nature Communications
- Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
- (2013) Mary A. Rohrdanz et al. Annual Review of Physical Chemistry
- Fast Tomographic Reconstruction From Limited Data Using Artificial Neural Networks
- (2013) Daniel Maria Pelt et al. IEEE TRANSACTIONS ON IMAGE PROCESSING
- Quantitative comparison of alternative methods for coarse-graining biological networks
- (2013) Gregory R. Bowman et al. JOURNAL OF CHEMICAL PHYSICS
- Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis
- (2013) Yusuke Naritomi et al. JOURNAL OF CHEMICAL PHYSICS
- Hierarchical Nyström methods for constructing Markov state models for conformational dynamics
- (2013) Yuan Yao et al. JOURNAL OF CHEMICAL PHYSICS
- Identification of slow molecular order parameters for Markov model construction
- (2013) Guillermo Pérez-Hernández et al. JOURNAL OF CHEMICAL PHYSICS
- Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules
- (2013) Frank Noé et al. JOURNAL OF CHEMICAL PHYSICS
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
- (2013) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
- (2013) Romelia Salomon-Ferrer et al. Journal of Chemical Theory and Computation
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
- (2013) Kai J. Kohlhoff et al. Nature Chemistry
- Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification
- (2013) Susanna Röblitz et al. Advances in Data Analysis and Classification
- A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
- (2013) Lin-Tai Da et al. PLoS Computational Biology
- To milliseconds and beyond: challenges in the simulation of protein folding
- (2012) Thomas J Lane et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- High-throughput molecular dynamics: the powerful new tool for drug discovery
- (2012) Matthew J. Harvey et al. DRUG DISCOVERY TODAY
- Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
- (2012) Gregory R. Bowman JOURNAL OF CHEMICAL PHYSICS
- Quantifying the rebinding effect in multivalent chemical ligand-receptor systems
- (2012) Marcus Weber et al. JOURNAL OF CHEMICAL PHYSICS
- Identifying Metastable States of Folding Proteins
- (2012) Abhinav Jain et al. Journal of Chemical Theory and Computation
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
- (2012) Peter Eastman et al. Journal of Chemical Theory and Computation
- A fast parallel clustering algorithm for molecular simulation trajectories
- (2012) Yutong Zhao et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
- (2012) Vincent A. Voelz et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Path Finding on High-Dimensional Free Energy Landscapes
- (2012) Grisell Díaz Leines et al. PHYSICAL REVIEW LETTERS
- Simple few-state models reveal hidden complexity in protein folding
- (2012) K. A. Beauchamp et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
- (2012) Eva Chovancova et al. PLoS Computational Biology
- Markov state models based on milestoning
- (2011) Christof Schütte et al. JOURNAL OF CHEMICAL PHYSICS
- Markov models of molecular kinetics: Generation and validation
- (2011) Jan-Hendrik Prinz et al. JOURNAL OF CHEMICAL PHYSICS
- MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
- (2011) Kyle A. Beauchamp et al. Journal of Chemical Theory and Computation
- Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding)
- (2011) Riccardo Scalco et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II
- (2011) Lin-Tai Da et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
- (2011) I. Buch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
- (2011) Daniel-Adriano Silva et al. PLoS Computational Biology
- Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
- (2010) Gregory R. Bowman et al. Journal of Chemical Theory and Computation
- Everything you wanted to know about Markov State Models but were afraid to ask
- (2010) Vijay S. Pande et al. METHODS
- Atomistic View of the Conformational Activation of Src Kinase Using the String Method with Swarms-of-Trajectories
- (2009) Wenxun Gan et al. BIOPHYSICAL JOURNAL
- Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
- (2009) Sergio Bacallado et al. JOURNAL OF CHEMICAL PHYSICS
- Progress and challenges in the automated construction of Markov state models for full protein systems
- (2009) Gregory R. Bowman et al. JOURNAL OF CHEMICAL PHYSICS
- Using generalized ensemble simulations and Markov state models to identify conformational states
- (2009) Gregory R. Bowman et al. METHODS
- Transition Path Theory for Markov Jump Processes
- (2009) Philipp Metzner et al. MULTISCALE MODELING & SIMULATION
- Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data
- (2009) Philipp Metzner et al. PHYSICAL REVIEW E
- Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
- (2009) Frank Noé et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
- (2008) Weinan E et al. Annual Review of Physical Chemistry
- Anton, a special-purpose machine for molecular dynamics simulation
- (2008) David E. Shaw et al. COMMUNICATIONS OF THE ACM
- Building Markov state models along pathways to determine free energies and rates of transitions
- (2008) Albert C. Pan et al. JOURNAL OF CHEMICAL PHYSICS
- An integrate-over-temperature approach for enhanced sampling
- (2008) Yi Qin Gao JOURNAL OF CHEMICAL PHYSICS
- Can Morphing Methods Predict Intermediate Structures?
- (2008) Dahlia R. Weiss et al. JOURNAL OF MOLECULAR BIOLOGY
- Finding Transition Pathways Using the String Method with Swarms of Trajectories
- (2008) Albert C. Pan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Coarse Master Equations for Peptide Folding Dynamics†
- (2008) Nicolae-Viorel Buchete et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
- (2008) L. Zheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started