4.6 Review

Structural genomics and the Protein Data Bank

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Covid-19.bioreproducibility.org: A web resource forSARS-CoV-2-related structural models

Dariusz Brzezinski et al.

Summary: The COVID-19 pandemic has sparked scientific activities to understand the SARS-CoV-2 virus and develop treatments. Structural biologists have identified hundreds of experimental structures related to this coronavirus, and a new online resource, covid19.bioreproducibility.org, provides expert-verified information about these models for biomedical researchers.

PROTEIN SCIENCE (2021)

Article Biochemistry & Molecular Biology

CATH: increased structural coverage of functional space

Ian Sillitoe et al.

Summary: CATH identifies protein domains in structures and classifies them into evolutionary superfamilies, providing structural and functional annotations. The latest release significantly increases coverage of structural and sequence data, with additional derived data such as predicted sequence domains and functionally coherent sequence subsets. The FunFam generation pipeline has been re-engineered to capture more sequences with increased functional purity and information content.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

Jerzy Osipiuk et al.

Summary: The study focused on papain-like protease (PLpro) as a potential target for antivirals against SARS-CoV-2, identifying inhibitors and their interactions with the enzyme. The findings demonstrate the potential for developing high-affinity inhibitors through structure-based drug design efforts targeting PLpro.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

ProMod3-A versatile homology modelling toolbox

Gabriel Studer et al.

Summary: Computational methods for protein structure modelling, especially homology modelling, play a crucial role in complementing experimental structure determination and generating accurate protein models. ProMod3 is a versatile software package designed for modelling protein structures by homology, empowering the widely used SWISS-MODEL webserver and providing millions of protein structure models to the scientific community.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Biology

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Youngchang Kim et al.

Summary: SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease that interferes with the innate immune response and is a potential target for therapeutic intervention. Studies have shown that Tipiracil inhibits the activity of Nsp15 by interacting with the uridine binding pocket. This discovery provides new insights for the development of drugs based on uracil scaffold.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

Article Biochemistry & Molecular Biology

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2

Youngchang Kim et al.

PROTEIN SCIENCE (2020)

Review Chemistry, Multidisciplinary

The data universe of structural biology

Helen M. Berman et al.

IUCRJ (2020)

Article Chemistry, Multidisciplinary

Crystal structures of SARS-CoV-2 ADP-ribose phosnhatase: from the apo form to ligand complexes

Karolina Michalska et al.

IUCRJ (2020)

News Item Multidisciplinary Sciences

STRUCTURAL BIOLOGY 'The game has changed.' AI triumphs at protein folding

Robert F. Service

SCIENCE (2020)

Review Biochemistry & Molecular Biology

Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be

Giuseppina Mariano et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2020)

Article Chemistry, Multidisciplinary

Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data

Jan Zaucha et al.

CHEMICAL COMMUNICATIONS (2020)

Review Biochemistry & Molecular Biology

Critical assessment of methods of protein structure prediction (CASP)-Round XIII

Andriy Kryshtafovych et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

Letter Biotechnology & Applied Microbiology

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P. Arkin et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme

Nan Wang et al.

NATURE CHEMICAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

TSTMP: target selection for structural genomics of human transmembrane proteins

Julia Varga et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily

Gaelle Batot et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Validation of Structures in the Protein Data Bank

Swanand Gore et al.

STRUCTURE (2017)

Letter Biochemistry & Molecular Biology

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

Stephen K. Burley et al.

STRUCTURE (2017)

Article Biochemistry & Molecular Biology

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Paul D. Adams et al.

STRUCTURE (2016)

Article Biochemical Research Methods

A public database of macromolecular diffraction experiments

Marek Grabowski et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

MolProbity for the masses-of data

Vincent B. Chen et al.

JOURNAL OF BIOMOLECULAR NMR (2015)

Article Biochemistry & Molecular Biology

DNASU plasmid and PSI: Biology-Materials repositories: resources to accelerate biological research

Catherine Y. Seiler et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

Covering complete proteomes with X-ray structures: a current snapshot

Marcin J. Mizianty et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

How Community Has Shaped the Protein Data Bank

Helen M. Berman et al.

STRUCTURE (2013)

Article Multidisciplinary Sciences

Principles for designing ideal protein structures

Nobuyasu Koga et al.

NATURE (2012)

Review Biochemical Research Methods

High-throughput protein purification and quality assessment for crystallization

Youngchang Kim et al.

METHODS (2011)

Article Biophysics

1,000 structures and more from the MCSG

David Lee et al.

BMC STRUCTURAL BIOLOGY (2011)

Article Mathematical & Computational Biology

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

Wolfgang F. Bluhm et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2011)

Article Biochemical Research Methods

The JCSG high-throughput structural biology pipeline

Marc-Andre Elsliger et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2010)

Article Biochemistry & Molecular Biology

The protein structure initiative structural genomics knowledgebase

Helen M. Berman et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

Nature of the protein universe

Michael Levitt

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Biochemical Research Methods

Protein production and purification

Susanne Graslund et al.

NATURE METHODS (2008)

Editorial Material Biochemistry & Molecular Biology

Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI production centers

Stephen K. Burley et al.

STRUCTURE (2008)

Article Biochemistry & Molecular Biology

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Ian W. Davis et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint

Russell L. Marsden et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Evaluating protein structures determined by structural genomics consortia

Aneerban Bhattacharya et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Growth of novel protein structural data

Michael Levitt

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemical Research Methods

HKL-3000:: the integration of data reduction and structure solution -: from diffraction images to an initial model in minutes

Wladek Minor et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2006)

Article Multidisciplinary Sciences

A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus

Joseph D. Mougous et al.

SCIENCE (2006)

Article Biochemistry & Molecular Biology

The RCSB PDB information portal for structural genomics

Andrei Kouranov et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

TargetDB: a target registration database for structural genomics projects

L Chen et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank

HW Yang et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

The Protein Data Bank and structural genomics

J Westbrook et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Structural genomics: A pipeline for providing structures for the biologist

MR Chance et al.

PROTEIN SCIENCE (2002)

Article Biochemistry & Molecular Biology

A rapid classification protocol for the CATH Domain Database to support structural genomics

FMG Pearl et al.

NUCLEIC ACIDS RESEARCH (2001)

Article Biochemistry & Molecular Biology

The Protein Data Bank and the challenge of structural genomics

HM Berman et al.

NATURE STRUCTURAL BIOLOGY (2000)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)