Computational protein design: The proteus software and selected applications

Rapid Calculation of Protein pKa Values Using Rosetta

(2012) Krishna Praneeth Kilambi et al.   BIOPHYSICAL JOURNAL

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Computational design of a protein crystal

(2012) C. J. Lanci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

Protein design in metabolic engineering and synthetic biology

(2011) Jürgen Pleiss   CURRENT OPINION IN BIOTECHNOLOGY

Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins

(2011) Jeffery G Saven   CURRENT OPINION IN CHEMICAL BIOLOGY

Recent advances in computational protein design

(2011) Robert J Pantazes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

(2011) Carie Fortenberry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease

(2011) M. R. Gunner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

(2011) Savvas Polydorides et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon

(2010) Travis S. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition

(2010) Marcel Schmidt am Busch et al.   PLoS One

Protein design automation

(2010) Bassil I. Dahiyat et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

De Novo Design of a βαβ Motif

(2009) Huanhuan Liang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Backbone flexibility in computational protein design

(2009) Daniel J Mandell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational protein design: Advances in the design and redesign of biomolecular nanostructures

(2009) Jeffery G. Saven   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Challenges in the computational design of proteins

(2009) M. Suarez et al.   Journal of the Royal Society Interface

Molecular determinants of the pKavalues of Asp and Glu residues in staphylococcal nuclease

(2009) Carlos A. Castañeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational protein design as a tool for fold recognition

(2009) Marcel Schmidt am Busch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design

(2008) Marcel am Busch et al.   BMC BIOINFORMATICS

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Computational protein design: Software implementation, parameter optimization, and performance of a simple model

(2007) Marcel Schmidt Am Busch et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An improved pairwise decomposable finite-difference Poisson–Boltzmann method for computational protein design

(2007) Christina L. Vizcarra et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY