Minireview: Applied Structural Bioinformatics in Proteomics
暂无分享,去创建一个
[1] Roland Arnold,et al. Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space , 2012, Methods.
[2] C. Mora,et al. How Many Species Are There on Earth and in the Ocean? , 2011, PLoS biology.
[3] D. Baker,et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.
[4] Nicholas A. Guziewicz,et al. X-ray and Biochemical Analysis of N370S Mutant Human Acid β-Glucosidase , 2010, The Journal of Biological Chemistry.
[5] L. Looger,et al. Computational design of receptor and sensor proteins with novel functions , 2003, Nature.
[6] Amol V. Shivange,et al. Reengineered carbonyl reductase for reducing methyl-substituted cyclohexanones. , 2013, Protein engineering, design & selection : PEDS.
[7] Jinhyuk Lee,et al. Computational Prediction of Protein-Protein Interactions of Human Tyrosinase , 2012, Enzyme research.
[8] Asa Ben-Hur,et al. Multiple instance learning of Calmodulin binding sites , 2012, Bioinform..
[9] Wen-Lian Hsu,et al. Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface , 2012, PloS one.
[10] D W Cushman,et al. Design of potent competitive inhibitors of angiotensin-converting enzyme. Carboxyalkanoyl and mercaptoalkanoyl amino acids. , 1977, Biochemistry.
[11] 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.
[12] Seren Soner,et al. Hot Spots in a Network of Functional Sites , 2013, PloS one.
[13] Ulrik B. Nielsen,et al. Antitumor Activity of a Novel Bispecific Antibody That Targets the ErbB2/ErbB3 Oncogenic Unit and Inhibits Heregulin-Induced Activation of ErbB3 , 2012, Molecular Cancer Therapeutics.
[14] A. Valencia,et al. Similarity of phylogenetic trees as indicator of protein-protein interaction. , 2001, Protein engineering.
[15] Marc N. Offman,et al. Molecular Basis of Reduced Glucosylceramidase Activity in the Most Common Gaucher Disease Mutant, N370S , 2010, The Journal of Biological Chemistry.
[16] Michal Brylinski,et al. eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands , 2013, Journal of Computer-Aided Molecular Design.
[17] Alessandro Gori,et al. Rational epitope design for protein targeting. , 2013, ACS chemical biology.
[18] Young Je Yoo,et al. Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent. , 2013, Journal of biotechnology.
[19] U. Sezerman,et al. Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. , 2013, Protein engineering, design & selection : PEDS.
[20] Matthew D. Dyer,et al. Supervised learning and prediction of physical interactions between human and HIV proteins. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[21] A. Valencia,et al. Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes , 1997, Journal of Molecular Evolution.
[22] Roy Lee Yung-Hung,et al. A 35 kDa antigenic protein from Shigella flexneri: in silico structural and functional studies. , 2011, Biochemical and biophysical research communications.
[23] Lodewyk F. A. Wessels,et al. A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer , 2011, PloS one.
[24] D. Baker,et al. Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope , 2011, Journal of Molecular Biology.
[25] Juan Fernández-Recio,et al. Prediction of protein-binding areas by small-world residue networks and application to docking , 2011, BMC Bioinformatics.
[26] Joan Segura,et al. A holistic in silico approach to predict functional sites in protein structures , 2012, Bioinform..
[27] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[28] C. García-echeverría,et al. Inhibitors of the p53/hdm2 protein-protein interaction-path to the clinic. , 2013, Bioorganic & medicinal chemistry letters.
[29] J. Trudell,et al. Charge and Geometry of Residues in the Loop 2 β Hairpin Differentially Affect Agonist and Ethanol Sensitivity in Glycine Receptors , 2012, Journal of Pharmacology and Experimental Therapeutics.
[30] Peter L. Freddolino,et al. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. , 2006, Structure.
[31] James O. Wrabl,et al. Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations. , 2013, Topics in current chemistry.
[32] J. Eswaran,et al. Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug efflux protein TolC. , 2004, Journal of molecular biology.
[33] Dengke Yin,et al. Prediction and Identification of Potential Immunodominant Epitopes in Glycoproteins B, C, E, G, and I of Herpes Simplex Virus Type 2 , 2012, Clinical & developmental immunology.
[34] Anat Burkovitz,et al. Computational Identification of Antigen-Binding Antibody Fragments , 2013, The Journal of Immunology.
[35] H. K. Fung,et al. De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation. , 2012, Journal of medicinal chemistry.
[36] Carolina Perez-Iratxeta,et al. Towards completion of the Earth's proteome , 2007, EMBO reports.
[37] Giovanni Da San Martino,et al. Improving biomarker list stability by integration of biological knowledge in the learning process , 2012, BMC Bioinformatics.
[38] F. Squina,et al. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. , 2013, Biochimica et biophysica acta.
[39] J J Baldwin,et al. Carbonic anhydrase inhibitors for the treatment of glaucoma , 2023, Медицинская этика.
[40] Marc N. Offman,et al. Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity. , 2011, Blood.
[41] Amol V. Shivange,et al. Design of an activity and stability improved carbonyl reductase from Candida parapsilosis. , 2013, Journal of biotechnology.
[42] Luigi Calzolai,et al. Rational Engineering of a Human Anti-Dengue Antibody through Experimentally Validated Computational Docking , 2013, PloS one.
[43] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[44] Arieh Warshel,et al. Bicycle-pedal model for the first step in the vision process , 1976, Nature.
[45] M. Levitt,et al. Computer simulation of protein folding , 1975, Nature.
[46] Martin Weigt,et al. Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis , 2012, Proceedings of the National Academy of Sciences.
[47] Liam J. McGuffin,et al. FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions , 2012, PloS one.
[48] Elizabeth Yuriev,et al. AutoMap: a tool for analyzing protein-ligand recognition using multiple ligand binding modes. , 2013, Journal of molecular graphics & modelling.
[49] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[50] Lisa Yan,et al. pH-selective mutagenesis of protein–protein interfaces: In silico design of therapeutic antibodies with prolonged half-life , 2012, Proteins.
[51] P. Luthra,et al. Insilico study of the A2AR–D2R kinetics and interfacial contact surface for heteromerization , 2012, Amino Acids.
[52] Sharmila Anishetty,et al. A matrix based algorithm for Protein-Protein Interaction prediction using Domain-Domain Associations. , 2013, Journal of theoretical biology.
[53] Binsheng Gong,et al. Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis , 2012, Journal of Neuro-Oncology.
[54] S. Cramer,et al. Design of peptide affinity ligands for S-protein: a comparison of combinatorial and de novo design strategies , 2013, Molecular Diversity.
[55] Y. Choong,et al. Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii , 2012, BMC Structural Biology.
[56] J. Orange,et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases , 2008, Nature Biotechnology.
[57] A. Abate,et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.
[58] Lei Xie,et al. Structure-based systems biology for analyzing off-target binding. , 2011, Current opinion in structural biology.
[59] Morgan L. Maeder,et al. Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.
[60] Marc Ostermeier,et al. A hot-spot motif characterizes the interface between a designed ankyrin-repeat protein and its target ligand. , 2012, Biophysical journal.
[61] Joo‐Hang Kim,et al. Novel cancer antiangiotherapy using the VEGF promoter-targeted artificial zinc-finger protein and oncolytic adenovirus. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.
[62] D. Dimitrov,et al. Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing , 2012, Front. Microbio..
[63] Hiroaki Kitano,et al. Large-Scale Analysis of Network Bistability for Human Cancers , 2010, PLoS Comput. Biol..
[64] Erkki Ruoslahti,et al. De novo design of a tumor-penetrating peptide. , 2013, Cancer research.
[65] K. Réblová,et al. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops. , 2013, The journal of physical chemistry. B.
[66] J. Mascola,et al. Progress in the rational design of an AIDS vaccine , 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.
[67] G. Sandstrom,et al. A potential in silico antibody-antigen based diagnostic test for precise identification of Acinetobacter baumannii. , 2012, Journal of theoretical biology.
[68] Y. Choong,et al. Structural and functional studies of a 50 kDa antigenic protein from Salmonella enterica serovar Typhi. , 2011, Journal of molecular graphics & modelling.