Toward structure prediction of cyclic peptides

Improving on Nature: Making a Cyclic Heptapeptide Orally Bioavailable

(2014) Daniel S. Nielsen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structured Cyclic Peptides That Bind the EH Domain of EHD1

(2014) Alissa J. Kamens et al.   BIOCHEMISTRY

Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models

(2014) Asghar M. Razavi et al.   Journal of Chemical Information and Modeling

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

(2014) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

Bayesian inference of conformational state populations from computational models and sparse experimental observables

(2014) Vincent A. Voelz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L

(2014) Fan Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model

(2013) João M. Damas et al.   Journal of Chemical Theory and Computation

Cyclic Peptide Inhibitors of HIV-1 Capsid-Human Lysyl-tRNA Synthetase Interaction

(2012) Varun Dewan et al.   ACS Chemical Biology

Intestinal Permeability of Cyclic Peptides: Common Key Backbone Motifs Identified

(2012) Johannes G. Beck et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

De novo structure prediction and experimental characterization of folded peptoid oligomers

(2012) G. L. Butterfoss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues

(2011) Jérôme Beaufays et al.   JOURNAL OF PEPTIDE SCIENCE

On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds

(2011) Tina R White et al.   Nature Chemical Biology

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

(2010) Sara R. R. Campos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

(2010) Abhinav Jain et al.   Journal of Physical Chemistry Letters

Improving replica exchange using driven scaling

(2009) Alexis J. Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring the Folding Free Energy Landscape of Insulin Using Bias Exchange Metadynamics

(2009) Nevena Todorova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Analysis in a Multidimensional Energy Landscape: Study of an Arginylglutamate Repeat

(2009) Sara R. R. Campos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Replica exchange with nonequilibrium switches

(2009) A. J. Ballard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Improving Oral Bioavailability of Peptides by Multiple N-Methylation: Somatostatin Analogues

(2008) Eric Biron et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The “Hot-Solvent/Cold-Solute” Problem Revisited

(2008) M. Lingenheil et al.   Journal of Chemical Theory and Computation

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats

(2008) Amit Mor et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The exploration of macrocycles for drug discovery — an underexploited structural class

(2008) Edward M. Driggers et al.   NATURE REVIEWS DRUG DISCOVERY

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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