SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity
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[1] Gábor Imre,et al. Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method , 2014, J. Chem. Inf. Model..
[2] George Papadatos,et al. The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..
[3] Gert Thijs,et al. Pharao: pharmacophore alignment and optimization. , 2008, Journal of molecular graphics & modelling.
[4] Ronald J Quinn,et al. Identification of Protein Fold Topology Shared between Different Folds Inhibited by Natural Products , 2007, Chembiochem : a European journal of chemical biology.
[5] Yuedong Yang,et al. Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome , 2014, PloS one.
[6] Yang Zhang,et al. BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions , 2012, Nucleic Acids Res..
[7] J. Irwin,et al. Benchmarking sets for molecular docking. , 2006, Journal of medicinal chemistry.
[8] Yuedong Yang,et al. Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome , 2014, Proteins.
[9] Arthur J. Olson,et al. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..
[10] Kiichi Tanimoto. ON THE DENSITY VARIATION IN SOIL BY COMPACTION , 1958 .
[11] Jeffrey Skolnick,et al. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score , 2008, BMC Bioinformatics.
[12] David S. Wishart,et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..
[13] Jeffrey Skolnick,et al. FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. , 2012, Molecular pharmaceutics.
[14] Michal Brylinski,et al. Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening , 2010, J. Chem. Inf. Model..
[15] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[16] Brian K. Shoichet,et al. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..
[17] Daisuke Kihara,et al. Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery , 2015, Molecules.
[18] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[19] J. A. Grant,et al. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. , 2005, Journal of medicinal chemistry.
[20] Andreas Bender,et al. Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance , 2004, J. Chem. Inf. Model..
[21] Hongyi Zhou,et al. FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach , 2013, J. Chem. Inf. Model..
[22] Yanli Wang,et al. Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review , 2012, The AAPS Journal.
[23] Yaoqi Zhou,et al. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function , 2010, Bioinform..
[24] Yaoqi Zhou,et al. Carbohydrate‐binding protein identification by coupling structural similarity searching with binding affinity prediction , 2014, J. Comput. Chem..
[25] A. Harvey,et al. The re-emergence of natural products for drug discovery in the genomics era , 2015, Nature Reviews Drug Discovery.
[26] Yuedong Yang,et al. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction , 2011, RNA biology.
[27] Michael M. Mysinger,et al. Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking , 2012, Journal of medicinal chemistry.
[28] Jeffrey Skolnick,et al. PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity , 2015, J. Chem. Inf. Model..
[29] David Vidal,et al. Ligand-based approaches to in silico pharmacology. , 2011, Methods in molecular biology.
[30] C. E. Peishoff,et al. A critical assessment of docking programs and scoring functions. , 2006, Journal of medicinal chemistry.
[31] Yaoqi Zhou,et al. A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction , 2012, Proteins.
[32] Yaoqi Zhou,et al. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates , 2011, Bioinform..
[33] J. Skolnick,et al. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation , 2008, Proceedings of the National Academy of Sciences.
[34] B. Shoichet,et al. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. , 2003, Journal of medicinal chemistry.
[35] I. Kuntz,et al. DOCK 6: combining techniques to model RNA-small molecule complexes. , 2009, RNA.