Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

(2013) Zhixiu Li et al.   Annual Review of Biophysics

Structure-Based Redesign of the Binding Specificity of Anti-Apoptotic Bcl-xL

(2012) T. Scott Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

(2011) Eshel Faraggi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations

(2011) Liang Dai et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

(2010) B. D. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering a protein-protein interface using a computationally designed library

(2010) G. Guntas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving computational protein design by using structure-derived sequence profile

(2010) Liang Dai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Challenges in the computational design of proteins

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

Computational protein design as a tool for fold recognition

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

Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction

(2009) Eshel Faraggi et al.   STRUCTURE

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

(2008) Eshel Faraggi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE