PredHS: a web server for predicting protein–protein interaction hot spots by using structural neighborhood properties
暂无分享,去创建一个
Zhigang Chen | Shuigeng Zhou | Jihong Guan | Lei Deng | Yang Meng | Qiangfeng Cliff Zhang | J. Guan | Q. Zhang | L. Deng | Shuigeng Zhou | Yang Meng | Zhigang Chen
[1] David P. Dobkin,et al. The quickhull algorithm for convex hulls , 1996, TOMS.
[2] Hiroyuki Ogata,et al. AAindex: Amino Acid Index Database , 1999, Nucleic Acids Res..
[3] Peter A. Kollman,et al. Computational alanine scanning of the 1:1 human growth hormone–receptor complex , 2002, J. Comput. Chem..
[4] Shuigeng Zhou,et al. Prediction of protein-protein interaction sites using an ensemble method , 2009, BMC Bioinformatics.
[5] Ozlem Keskin,et al. HotSprint: database of computational hot spots in protein interfaces , 2007, Nucleic Acids Res..
[6] Michael J. Hartshorn,et al. AstexViewerTM †: a visualisation aid for structure-based drug design , 2002, J. Comput. Aided Mol. Des..
[7] T. Clackson,et al. A hot spot of binding energy in a hormone-receptor interface , 1995, Science.
[8] Julie C. Mitchell,et al. An automated decision‐tree approach to predicting protein interaction hot spots , 2007, Proteins.
[9] D. Bailey,et al. The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces , 2003, Bioinform..
[10] Michael J Hartshorn,et al. AstexViewer: a visualisation aid for structure-based drug design. , 2002, Journal of computer-aided molecular design.
[11] Joan Segura,et al. PCRPi-DB: a database of computationally annotated hot spots in protein interfaces , 2010, Nucleic Acids Res..
[12] G. Hong,et al. Nucleic Acids Research , 2015, Nucleic Acids Research.
[13] Christopher L. McClendon,et al. Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.
[14] Salam A. Assi,et al. PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces , 2009, Nucleic acids research.
[15] Dima Kozakov,et al. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques , 2009, Bioinform..
[16] Andy Liaw,et al. Classification and Regression by randomForest , 2007 .
[17] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.
[18] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[19] Pamela F. Jones,et al. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams , 2011, BMC Bioinformatics.
[20] Kurt S. Thorn,et al. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..
[21] Doheon Lee,et al. A feature-based approach to modeling protein–protein interaction hot spots , 2009, Nucleic acids research.
[22] Franziska Hoffmann,et al. Spatial Tessellations Concepts And Applications Of Voronoi Diagrams , 2016 .
[23] Ozlem Keskin,et al. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy , 2009, Bioinform..
[24] Shuigeng Zhou,et al. Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties , 2013, J. Comput. Biol..
[25] Yu-Dong Cai,et al. Cooperativity among Short Amyloid Stretches in Long Amyloidogenic Sequences , 2012, PloS one.
[26] Nick V Grishin,et al. Effective scoring function for protein sequence design , 2003, Proteins.
[27] Emmanuel D Levy,et al. PiQSi: protein quaternary structure investigation. , 2007, Structure.
[28] Julie C. Mitchell,et al. KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features , 2011, Proteins.
[29] Chenhsiung Chan,et al. Relationship between local structural entropy and protein thermostabilty , 2004, Proteins.
[30] Xiang-Sun Zhang,et al. Prediction of hot spots in protein interfaces using a random forest model with hybrid features. , 2012, Protein engineering, design & selection : PEDS.
[31] O. Ptitsyn,et al. Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions , 1998, Protein science : a publication of the Protein Society.
[32] Burkhard Rost,et al. Protein–Protein Interaction Hotspots Carved into Sequences , 2007, PLoS Comput. Biol..
[33] Ozlem Keskin,et al. HotPoint: hot spot prediction server for protein interfaces , 2010, Nucleic Acids Res..
[34] Solène Grosdidier,et al. Identification of hot-spot residues in protein-protein interactions by computational docking , 2008, BMC Bioinformatics.
[35] Alexander Tropsha,et al. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations , 2003, Bioinform..
[36] Ozlem Keskin,et al. HotRegion: a database of predicted hot spot clusters , 2011, Nucleic Acids Res..
[37] D. Baker,et al. A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[38] P. Kollman,et al. Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies , 1999 .
[39] Xing-Ming Zhao,et al. APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility , 2010, BMC Bioinformatics.
[40] Chih-Jen Lin,et al. LIBSVM: A library for support vector machines , 2011, TIST.