Enhancing Sampling of the Conformational Space Near the Protein Native State

[1]  Amarda Shehu,et al.  Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration , 2010, Int. J. Robotics Res..

[2]  L. Kavraki,et al.  Multiscale characterization of protein conformational ensembles , 2009, Proteins.

[3]  Amarda Shehu,et al.  An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations , 2009, Robotics: Science and Systems.

[4]  James E. Fitzgerald,et al.  Mimicking the folding pathway to improve homology-free protein structure prediction , 2009, Proceedings of the National Academy of Sciences.

[5]  Oliver Brock,et al.  Guiding conformation space search with an all‐atom energy potential , 2008, Proteins.

[6]  Cecilia Clementi,et al.  Unfolding the fold of cyclic cysteine‐rich peptides , 2008, Protein science : a publication of the Protein Society.

[7]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[8]  K. Dill,et al.  The protein folding problem. , 1993, Annual review of biophysics.

[9]  Wolfram Burgard,et al.  Discrete Search Leading Continuous Exploration for Kinodynamic Motion Planning , 2008 .

[10]  David A. Lee,et al.  Predicting protein function from sequence and structure , 2007, Nature Reviews Molecular Cell Biology.

[11]  Lydia E Kavraki,et al.  From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes , 2007, Proteins.

[12]  W. Graham Richards,et al.  Ultrafast shape recognition to search compound databases for similar molecular shapes , 2007, J. Comput. Chem..

[13]  Lydia E. Kavraki,et al.  Discrete Search Leading Continuous Exploration for Kinodynamic Motion Planning , 2007, Robotics: Science and Systems.

[14]  B. Matthews.  Protein Structure Initiative: getting into gear , 2007, Nature Structural &Molecular Biology.

[15]  Shuangye Yin,et al.  Eris: an automated estimator of protein stability , 2007, Nature Methods.

[16]  James J. Kuffner,et al.  Planning Among Movable Obstacles with Artificial Constraints , 2008, Int. J. Robotics Res..

[17]  Nancy M. Amato,et al.  RESAMPL: A Region-Sensitive Adaptive Motion Planner , 2008, WAFR.

[18]  David Hsu,et al.  Workspace-Based Connectivity Oracle: An Adaptive Sampling Strategy for PRM Planning , 2006, WAFR.

[19]  Gaetano T. Montelione,et al.  3.11 News & Views 031 CDS , 2005 .

[20]  P. Bradley,et al.  Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.

[21]  Oliver Brock,et al.  Efficient Motion Planning Based on Disassembly , 2005, Robotics: Science and Systems.

[22]  Lydia E. Kavraki,et al.  Motion Planning in the Presence of Drift, Underactuation and Discrete System Changes , 2005, Robotics: Science and Systems.

[23]  Howie Choset,et al.  Principles of Robot Motion: Theory, Algorithms, and Implementation ERRATA!!!! 1 , 2007 .

[24]  Mark H. Overmars,et al.  Using Workspace Information as a Guide to Non-uniform Sampling in Probabilistic Roadmap Planners , 2004, IEEE International Conference on Robotics and Automation, 2004. Proceedings. ICRA '04. 2004.

[25]  Tanja Kortemme,et al.  Computational design of protein-protein interactions. , 2004, Current opinion in chemical biology.

[26]  Adrian A Canutescu,et al.  Access the most recent version at doi: 10.1110/ps.03154503 References , 2003 .

[27]  Guoli Wang,et al.  PISCES: a protein sequence culling server , 2003, Bioinform..

[28]  H. Wolfson,et al.  Reducing the computational complexity of protein folding via fragment folding and assembly , 2003, Protein science : a publication of the Protein Society.

[29]  M. Levitt,et al.  Small libraries of protein fragments model native protein structures accurately. , 2002, Journal of molecular biology.

[30]  Richard Bonneau,et al.  De novo prediction of three-dimensional structures for major protein families. , 2002, Journal of molecular biology.

[31]  Jean-Claude Latombe,et al.  On Delaying Collision Checking in PRM Planning: Application to Multi-Robot Coordination , 2002, Int. J. Robotics Res..

[32]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[33]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[34]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[35]  S. Rackovsky,et al.  Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. , 1998, Biopolymers.

[36]  Jooyoung Lee,et al.  New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997, J. Comput. Chem..

[37]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[38]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[39]  P. Wolynes,et al.  The energy landscapes and motions of proteins. , 1991, Science.

[40]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.