Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates?
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July 2016 |
De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers
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April 2009 |
De Novo Design of Antimicrobial Polymers, Foldamers, and Small Molecules: From Discovery to Practical Applications
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January 2010 |
A Rationally Designed Aldolase Foldamer
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January 2009 |
Folded biomimetic oligomers for enantioselective catalysis
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August 2009 |
Foldamer-Based Molecular Recognition
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March 2000 |
Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer
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July 2008 |
Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers
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April 2010 |
Foldamers: A Manifesto
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April 1998 |
A Field Guide to Foldamers
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December 2001 |
Aromatic Oligoamide Foldamers
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January 2004 |
Beyond de novo protein design — de novo design of non-natural folded oligomers
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August 2004 |
Foldamers as versatile frameworks for the design and evolution of function
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April 2007 |
Foldamers with Heterogeneous Backbones
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October 2008 |
Recent advances in the development of aryl-based foldamers
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January 2009 |
α/β-Peptide foldamers: state of the art
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April 2011 |
Synthetic foldamers
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January 2011 |
Aromatic Amide Foldamers: Structures, Properties, and Functions
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June 2012 |
Peptidic foldamers: ramping up diversity
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January 2012 |
Enhanced sampling techniques in molecular dynamics simulations of biological systems
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May 2015 |
Advances in enhanced sampling molecular dynamics simulations for biomolecules
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June 2019 |
Statistically optimal analysis of samples from multiple equilibrium states
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September 2008 |
Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting
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February 2016 |
Protein storytelling through physics
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November 2020 |
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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May 2017 |
Deep learning methods in protein structure prediction
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journal
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January 2020 |
New developments in force fields for biomolecular simulations
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journal
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April 2018 |
Minimalist models for proteins: a comparative analysis
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August 2010 |
Coarse-Grained Protein Models and Their Applications
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journal
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June 2016 |
Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
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journal
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March 2009 |
Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
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August 2003 |
A Multiscale Coarse-Graining Method for Biomolecular Systems
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February 2005 |
Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach
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May 2020 |
Computer simulation of protein folding
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February 1975 |
Principles of protein folding - A perspective from simple exact models
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April 1995 |
Protein Folding Thermodynamics and Dynamics: Where Physics, Chemistry, and Biology Meet
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May 2006 |
Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide Model
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April 2006 |
Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach
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June 2007 |
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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July 2017 |
Replica-exchange molecular dynamics method for protein folding
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journal
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November 1999 |
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
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journal
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January 2007 |
Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods
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journal
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October 2019 |
Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations
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journal
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May 2008 |
Exchange frequency in replica exchange molecular dynamics
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January 2008 |
On the acceptance probability of replica-exchange Monte Carlo trials
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October 2002 |
Optimal allocation of replicas in parallel tempering simulations
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January 2005 |
A constant entropy increase model for the selection of parallel tempering ensembles
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journal
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May 2008 |
Optimized parallel tempering simulations of proteins
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May 2006 |
On the Efficiency of Exchange in Parallel Tempering Monte Carlo Simulations
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February 2005 |
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
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November 2011 |
Accelerating molecular dynamic simulation on graphics processing units
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April 2009 |
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
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January 2009 |
SciPy 1.0: fundamental algorithms for scientific computing in Python
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February 2020 |
Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles
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December 2012 |
Testing for physical validity in molecular simulations
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September 2018 |
An Introduction to the Bootstrap
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book
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January 1993 |
Clustering algorithms to analyze molecular dynamics simulation trajectories for complex chemical and biological systems
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August 2018 |
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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October 2015 |
DBSCAN Revisited, Revisited: Why and How You Should (Still) Use DBSCAN
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August 2017 |
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
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December 2013 |
Simple data and workflow management with the signac framework
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April 2018 |
Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
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January 2014 |
Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference
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March 2019 |