Comprehensive computational design of ordered peptide macrocycles

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

(2016) Liulin Deng et al.   ANALYTICAL CHEMISTRY

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Accurate de novo design of hyperstable constrained peptides

(2016) Gaurav Bhardwaj et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

(2016) S. E. Boyken et al.   SCIENCE

Peptide therapeutics: current status and future directions

(2015) Keld Fosgerau et al.   DRUG DISCOVERY TODAY

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

(2015) Po-Ssu Huang et al.   Nature Chemical Biology

The Emergence of Cyclic Peptides: The Potential of Bioengineered Peptide Drugs

(2014) Parashar Thapa et al.   International Journal of Peptide Research and Therapeutics

Comprehensive analysis of loops at protein-protein interfaces for macrocycle design

(2014) Jason Gavenonis et al.   Nature Chemical Biology

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

MSMExplorer: visualizing Markov state models for biomolecule folding simulations

(2013) B. Cronkite-Ratcliff et al.   BIOINFORMATICS

Combinatorial Peptide Libraries: Mining for Cell-Binding Peptides

(2013) Bethany Powell Gray et al.   CHEMICAL REVIEWS

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández 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

The Future of Peptide-based Drugs

(2012) David J. Craik et al.   Chemical Biology & Drug Design

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

Algorithm discovery by protein folding game players

(2011) F. Khatib et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calibur: a tool for clustering large numbers of protein decoys

(2010) Shuai Cheng Li et al.   BMC BIOINFORMATICS

A New Clustering of Antibody CDR Loop Conformations

(2010) Benjamin North et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

Past and Future Perspectives of Synthetic Peptide Libraries

(2008) Daniela Marasco et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

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

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

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE