Mapping the sequence–structure relationships of simple cyclic hexapeptides

Insights into How Cyclic Peptides Switch Conformations

(2016) Sean M. McHugh et al.   Journal of Chemical Theory and Computation

PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems

(2016) Markus Fleck et al.   Journal of Chemical Theory and Computation

Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields

(2016) Hao Geng et al.   Journal of Physical Chemistry Letters

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins

(2016) David H. Brookes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Flexibility versus Rigidity for Orally Bioavailable Cyclic Hexapeptides

(2015) Daniel S. Nielsen et al.   CHEMBIOCHEM

Metadynamics Simulations Rationalise the Conformational Effects Induced byN-Methylation of RGD Cyclic Hexapeptides

(2015) Cristina Paissoni et al.   CHEMISTRY-A EUROPEAN JOURNAL

Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides

(2015) Amanda E. Wakefield et al.   Journal of Chemical Information and Modeling

Diversification of β-Augmentation Interactions between CDI Toxin/Immunity Proteins

(2015) Robert P. Morse et al.   JOURNAL OF MOLECULAR BIOLOGY

Toward structure prediction of cyclic peptides

(2015) Hongtao Yu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Targeting DnaN for tuberculosis therapy using novel griselimycins

(2015) A. Kling et al.   SCIENCE

A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake

(2014) Justin S. Quartararo et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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

Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants

(2014) Eugene Yedvabny et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB

(2014) Chen-Yang Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent-induced conformational changes in cyclic peptides: a vibrational circular dichroism study

(2014) Christian Merten et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Computational and Experimental Investigations into the Conformations of Cyclic Tetra-α/β-peptides

(2013) Mark T. Oakley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Visualizing Cyclic Peptide Hydration at the Single-Molecule Level

(2013) Yumin Chen et al.   Scientific Reports

New cyclic peptides with osteoblastic proliferative activity from Dianthus superbus

(2012) Yun Tong et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling

(2012) Mark T. Oakley et al.   Journal of Chemical Theory and Computation

Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation

(2012) Bracken M. King et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intestinal Permeability of Cyclic Peptides: Common Key Backbone Motifs Identified

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

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding

(2012) A. T. Fenley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Use of Metadynamics in the Design of isoDGR-Based αvβ3 Antagonists To Fine-Tune the Conformational Ensemble

(2011) Andrea Spitaleri et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Experimental and computational insights into the conformations of tunicyclin E, a new cycloheptapeptide from Psammosilene tunicoides

(2011) Jun-Mian Tian et al.   RSC Advances

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

(2010) Vincent A. Voelz et al.   BIOPOLYMERS

MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets

(2009) Bracken M. King et al.   BIOINFORMATICS

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