Andreas Prlić
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Development and application of a computable genotype model in the GA4GH Variation Representation Specification Open
As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinic…
Development and application of a computable genotype model in the GA4GH Variation Representation Specification Open
As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinic…
SeqRepo: A system for managing local collections of biological sequences Open
Motivation Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence…
Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1. Open
Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating …
SeqRepo: A system for managing local collections biological sequences Open
Motivation Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence…
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm Open
Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to th…
BioJava 5: A community driven open-source bioinformatics library Open
BioJava is an open-source project that provides a Java library for processing biological data. The project aims to simplify bioinformatic analyses by implementing parsers, data structures, and algorithms for common tasks in genomics, struc…
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular str…
hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update Open
The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in public variant databases and the scientific literature. Inconsistent applicatio…
Investigation of protein quaternary structure via stoichiometry and symmetry ınformation Open
The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by mo…
NGL viewer: web-based molecular graphics for large complexes Open
Motivation The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size. Results We …
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm Open
Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to th…
RCSB PDB: structural biology views for basic and applied research Open
tools for structure query, analysis, and visualization (Berman et al., 2000; Rose et al., 2017).Users can perform simple searches from the top search bar (e.g., ID, name, sequence, ligand) or build complex combinations of search parameters…
Quaternary structure evaluation tool for protein assemblies Open
The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by mo…
MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures Open
Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualiza…
MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures Open
Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualiza…
Towards an efficient compression of 3D coordinates of macromolecular structures Open
The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the vis…
Impact of genetic variation on three dimensional structure and function of proteins Open
The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 ex…
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank Open
Summary We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collecte…
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank Open
Summary: The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a …
OUP accepted manuscript Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computationa…