Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

The archiving and dissemination of biological structure data

(2016) Helen M Berman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits

(2016) Johannes Schiebel et al.   STRUCTURE

Molmil: a molecular viewer for the PDB and beyond

(2016) Gert-Jan Bekker et al.   Journal of Cheminformatics

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

(2016) Masashi Yokochi et al.   Journal of Biomedical Semantics

An ontology for major histocompatibility restriction

(2016) Randi Vita et al.   Journal of Biomedical Semantics

SPARQL-enabled identifier conversion with Identifiers.org

(2015) S. M. Wimalaratne et al.   BIOINFORMATICS

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB

(2015) Hirofumi Suzuki et al.   BIOINFORMATICS

Molecular fingerprint similarity search in virtual screening

(2015) Adrià Cereto-Massagué et al.   METHODS

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

(2015) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology

(2015) David S. Goodsell et al.   PLOS BIOLOGY

3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity

(2014) Takeshi Kawabata et al.   Journal of Chemical Information and Modeling

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

(2013) Hiroshi Wako et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A common type system for clinical natural language processing

(2013) Stephen T Wu et al.   Journal of Biomedical Semantics

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Dynamic features of homodimer interfaces calculated by normal-mode analysis

(2012) Yuko Tsuchiya et al.   PROTEIN SCIENCE

Build-Up Algorithm for Atomic Correspondence between Chemical Structures

(2011) Takeshi Kawabata   Journal of Chemical Information and Modeling

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

(2011) A. R. Kinjo et al.   NUCLEIC ACIDS RESEARCH

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

(2011) Axel Drefahl   Journal of Cheminformatics

SeSAW: balancing sequence and structural information in protein functional mapping

(2010) D. M. Standley et al.   BIOINFORMATICS

Geometric Similarities of Protein–Protein Interfaces at Atomic Resolution Are Only Observed within Homologous Families: An Exhaustive Structural Classification Study

(2010) Akira R. Kinjo et al.   JOURNAL OF MOLECULAR BIOLOGY

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

(2010) A. R. Kinjo et al.   Database-The Journal of Biological Databases and Curation

Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins

(2009) Akira R. Kinjo et al.   STRUCTURE

Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model

(2008) Takeshi Kawabata   BIOPHYSICAL JOURNAL

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS