Computational design of structured loops for new protein functions

New Deep Learning Methods for Protein Loop Modeling

(2017) Son Phong Nguyen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fast de novo discovery of low-energy protein loop conformations

(2017) Samuel W. K. Wong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Length-independent structural similarities enrich the antibody CDR canonical class model

(2016) Jaroslaw Nowak et al.   mAbs

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

(2016) James T. MacDonald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

(2015) Gideon D. Lapidoth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Experimental and Computational Mutagenesis To Investigate the Positioning of a General Base within an Enzyme Active Site

(2014) Jason P. Schwans et al.   BIOCHEMISTRY

LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains

(2013) Shide Liang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling Structures and Motions of Loops in Protein Molecules

(2012) Amarda Shehu et al.   Entropy

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy

(2011) Yaohang Li et al.   Journal of Chemical Information and Modeling

Assessing Protein Loop Flexibility by Hierarchical Monte Carlo Sampling

(2011) Jerome Nilmeier et al.   Journal of Chemical Theory and Computation

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

(2011) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational Optimization with Natural Degrees of Freedom: A Novel Stochastic Chain Closure Algorithm

(2010) Peter Minary et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Effects of somatic mutations on CDR loop flexibility during affinity maturation

(2010) Sergio E. Wong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein loop modeling by using fragment assembly and analytical loop closure

(2010) Julian Lee 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

Alteration of enzyme specificity by computational loop remodeling and design

(2009) P. M. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LOOPER: a molecular mechanics-based algorithm for protein loop prediction

(2008) V. Z. Spassov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS