Clustering Protein Conformations Using a Dynamic Programming Based Similarity Measurement

[1]  Osamu Miyashita,et al.  Simple energy landscape model for the kinetics of functional transitions in proteins. , 2005, The journal of physical chemistry. B.

[2]  Vijay S. Pande,et al.  Persistent Topology and Metastable State in Conformational Dynamics , 2013, PloS one.

[3]  Rafael Najmanovich,et al.  ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability , 2015, Nucleic Acids Res..

[4]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[5]  J. MacQueen.  Some methods for classification and analysis of multivariate observations , 1967 .

[6]  T. Caliński,et al.  A dendrite method for cluster analysis , 1974 .

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

[8]  L. Kavraki,et al.  SIMS: A Hybrid Method for Rapid Conformational Analysis , 2013, PloS one.

[9]  L. Kavraki,et al.  Tracing conformational changes in proteins , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop.

[10]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[11]  R. Jernigan,et al.  The energy profiles of atomic conformational transition intermediates of adenylate kinase , 2009, Proteins.

[12]  J. Tenenbaum,et al.  A global geometric framework for nonlinear dimensionality reduction. , 2000, Science.

[13]  J. Onuchic,et al.  Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.

[14]  Ora Schueler-Furman,et al.  Rapid Sampling of Molecular Motions with Prior Information Constraints , 2009, PLoS Comput. Biol..

[15]  Dan A. Simovici,et al.  Characterizing Intermediate Conformations in Protein Conformational Space , 2012, CIBB.

[16]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[17]  Amarda Shehu,et al.  Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method , 2013, BMC Structural Biology.

[18]  Amir Vajdi,et al.  A new DP algorithm for comparing gene expression data using geometric similarity , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

[20]  Mark A. Wilson,et al.  Intrinsic motions along an enzymatic reaction trajectory , 2007, Nature.

[21]  Dahlia R. Weiss,et al.  Can morphing methods predict intermediate structures? , 2009, Journal of molecular biology.

[22]  Nurit Haspel,et al.  Multi-Resolution Rigidity-Based Sampling of Protein Conformational Paths , 2013, BCB.

[23]  Guang Song,et al.  Protein elastic network models and the ranges of cooperativity , 2009, Proceedings of the National Academy of Sciences.