PDB-Explorer: a web-based interactive map of the protein data bank in shape space

[1]  Jean-Louis Reymond,et al.  Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces , 2015, J. Chem. Inf. Model..

[2]  Luc Patiny,et al.  Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia , 2015, Journal of Cheminformatics.

[3]  J. Reymond The chemical space project. , 2015, Accounts of chemical research.

[4]  Xian Jin,et al.  Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints , 2015, Journal of Cheminformatics.

[5]  David S. Goodsell,et al.  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..

[6]  Gert Vriend,et al.  A series of PDB related databases for everyday needs , 2010, Nucleic Acids Res..

[7]  Alexey G. Murzin,et al.  SCOP2 prototype: a new approach to protein structure mining , 2014, Nucleic Acids Res..

[8]  Jean-Louis Reymond,et al.  Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17 , 2014, J. Chem. Inf. Model..

[9]  A. Hopkins,et al.  The role of ligand efficiency metrics in drug discovery , 2014, Nature Reviews Drug Discovery.

[10]  Dachuan Zhang,et al.  MMDB and VAST+: tracking structural similarities between macromolecular complexes , 2013, Nucleic Acids Res..

[11]  Jean-Louis Reymond,et al.  SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules , 2013, J. Chem. Inf. Model..

[12]  Matthias Rarey,et al.  Protein pocket and ligand shape comparison and its application in virtual screening , 2013, Journal of Computer-Aided Molecular Design.

[13]  C. Ortiz Mellet,et al.  Cyclodextrin-based multivalent glycodisplays: covalent and supramolecular conjugates to assess carbohydrate-protein interactions. , 2013, Chemical Society reviews.

[14]  Jean-Louis Reymond,et al.  MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13 , 2013, J. Chem. Inf. Model..

[15]  David S. Goodsell,et al.  The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..

[16]  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.

[17]  Ryan G. Coleman,et al.  ZINC: A Free Tool to Discover Chemistry for Biology , 2012, J. Chem. Inf. Model..

[18]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[19]  W. Wade,et al.  Bergey’s Manual of Systematic Bacteriology , 2012 .

[20]  Tim A. H. te Beek,et al.  A series of PDB related databases for everyday needs , 2010, Nucleic Acids Res..

[21]  Ingvar C. Lagerstedt,et al.  PDBe: Protein Data Bank in Europe , 2010, Nucleic Acids Res..

[22]  Andreas Prlic,et al.  Pre-calculated protein structure alignments at the RCSB PDB website , 2010, Bioinform..

[23]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[24]  Michal Brylinski,et al.  Comparison of structure‐based and threading‐based approaches to protein functional annotation , 2010, Proteins.

[25]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[26]  F. Rey,et al.  Crystal Structure of an Aquabirnavirus Particle: Insights into Antigenic Diversity and Virulence Determinism , 2009, Journal of Virology.

[27]  Daisuke Kihara,et al.  3D-SURFER: software for high-throughput protein surface comparison and analysis , 2009, Bioinform..

[28]  Ian Sillitoe,et al.  The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space , 2009, Structure.

[29]  N. Verdaguer,et al.  Autoproteolytic Activity Derived from the Infectious Bursal Disease Virus Capsid Protein* , 2009, Journal of Biological Chemistry.

[30]  Ke Chen,et al.  Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions , 2009, PloS one.

[31]  Jeffrey Skolnick,et al.  Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score , 2008, BMC Bioinformatics.

[32]  Bin Li,et al.  Fast protein tertiary structure retrieval based on global surface shape similarity , 2008, Proteins.

[33]  Lenore Cowen,et al.  Matt: Local Flexibility Aids Protein Multiple Structure Alignment , 2008, PLoS Comput. Biol..

[34]  Tim J. P. Hubbard,et al.  Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..

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

[36]  Clemencia Pinilla,et al.  A Similarity‐based Data‐fusion Approach to the Visual Characterization and Comparison of Compound Databases , 2007, Chemical biology & drug design.

[37]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[38]  David J Craik,et al.  Chemical modification of conotoxins to improve stability and activity. , 2007, ACS chemical biology.

[39]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[40]  J. Pous,et al.  The 2.6-Angstrom Structure of Infectious Bursal Disease Virus-Derived T=1 Particles Reveals New Stabilizing Elements of the Virus Capsid , 2006, Journal of Virology.

[41]  Peter M Fischer,et al.  Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design. , 2006, Chemistry & biology.

[42]  Mark Gerstein,et al.  The Database of Macromolecular Motions: new features added at the decade mark , 2005, Nucleic Acids Res..

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

[44]  C. Orengo,et al.  Protein families and their evolution-a structural perspective. , 2005, Annual review of biochemistry.

[45]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[46]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

[47]  Dan S. Tawfik,et al.  Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. , 2003, Trends in biochemical sciences.

[48]  Wolfgang H. B. Sauer,et al.  Molecular Shape Diversity of Combinatorial Libraries: A Prerequisite for Broad Bioactivity , 2003, J. Chem. Inf. Comput. Sci..

[49]  G. Hammes Multiple conformational changes in enzyme catalysis. , 2002, Biochemistry.

[50]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[51]  Schmid,et al.  "Scaffold-Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. , 1999, Angewandte Chemie.

[52]  W. Pearson,et al.  Evolution of protein sequences and structures. , 1999, Journal of molecular biology.

[53]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[54]  M. Gerstein,et al.  A database of macromolecular motions. , 1998, Nucleic acids research.

[55]  Y. J. Sun,et al.  The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins. , 1998, Journal of molecular biology.

[56]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[57]  Y. J. Sun,et al.  The crystal structure of glutamine-binding protein from Escherichia coli. , 1996, Journal of molecular biology.

[58]  L. Johnson,et al.  Active and Inactive Protein Kinases: Structural Basis for Regulation , 1996, Cell.

[59]  D. Craik,et al.  The 1.1 A crystal structure of the neuronal acetylcholine receptor antagonist, alpha-conotoxin PnIA from Conus pennaceus. , 1996, Structure.

[60]  Robert P. Sheridan,et al.  Chemical Similarity Using Geometric Atom Pair Descriptors , 1996, J. Chem. Inf. Comput. Sci..

[61]  K Mizuguchi,et al.  Seeking significance in three-dimensional protein structure comparisons. , 1995, Current opinion in structural biology.

[62]  J Ramachandran,et al.  Solution structure of omega-conotoxin MVIIC, a high affinity ligand of P-type calcium channels, using 1H NMR spectroscopy and complete relaxation matrix analysis. , 1995, Journal of molecular biology.

[63]  T. P. Flores,et al.  Comparison of conformational characteristics in structurally similar protein pairs , 1993, Protein science : a publication of the Protein Society.

[64]  T. Blundell,et al.  Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.

[65]  R. Venkataraghavan,et al.  Atom pairs as molecular features in structure-activity studies: definition and applications , 1985, J. Chem. Inf. Comput. Sci..