4.6 Article

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Medicinal

Discovery of Small-Molecule Inhibitors of the PD-1/PD-L1 Axis That Promote PD-L1 Internalization and Degradation

Tianyu Wang et al.

Summary: Compound 17 is a bifunctional inhibitor that can block the interactions between PD-1 and PD-L1, promoting internalization and degradation of PD-L1. It effectively suppresses tumor growth in vivo by activating antitumor immunity.

JOURNAL OF MEDICINAL CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Database resources of the national center for biotechnology information

Eric W. Sayers et al.

Summary: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including databases for nucleic acid sequences and life science journal citations. It provides search and retrieval operations for most of these data from 35 distinct databases, with E-utilities serving as the programming interface. Several resources received significant updates in the past year.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Stephen K. Burley et al.

Summary: RCSB PDB, funded by several US government agencies, has been providing service to structural biologists and PDB data consumers worldwide since 1999. It is a founding member of the worldwide Protein Data Bank partnership, serving as the US data center for the global PDB archive. RCSB PDB also develops new tools and features for 3D structure analysis and visualization.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Gert-Jan Bekker et al.

Summary: Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB), has continuously improved and expanded its query search interface and services over the past 20 years, making significant contributions to the acceptance, processing, and distribution of experimentally determined biological macromolecular structures. During the COVID-19 pandemic, PDBj has also provided feature pages for COVID-19 related entries and outreach content for high school students and teachers.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

PDB-101: Educational resources supporting molecular explorations through biology and medicine

Christine Zardecki et al.

Summary: PDB-101 is an online portal created to support education, research, and promotion of structural biology and protein science. It provides materials for exploring atomic-level three-dimensional structures of biomolecules and aims to train the next generation of users.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

Simplified quality assessment for small-molecule ligands in the Protein Data Bank

Chenghua Shao et al.

Summary: This study analyzed quality indicators of small-molecule ligands in experimentally determined macromolecular structures in the Protein Data Bank (PDB). It found that ligand quality varies greatly in terms of fit to experimental data, deviations from known chemical structures, and interatomic clashes. A composite ranking score was constructed based on these quality indicators, allowing for comparison of chemically identical ligands in different PDB structures. Two-dimensional ligand quality plots were used to assess ligand structure quality and select the best exemplars.

STRUCTURE (2022)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens

David S. Goodsell et al.

Summary: Structural biologists play a crucial role in understanding human health and disease at the molecular level. The open access Protein Data Bank (PDB) stores and provides three-dimensional biostructure data to aid in the discovery and development of therapeutic agents and diagnostic tools. The success of non-infectious mRNA vaccines, such as those developed during the COVID-19 pandemic, is based on the knowledge of 3D viral protein structures. The RCSB PDB supports vaccine designers through rigorous validation and dissemination of structure information, as well as providing tools for structure-guided design efforts.

STRUCTURE (2022)

Article Biochemical Research Methods

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Joan Segura et al.

Summary: This article presents a new library that allows for customizable interactive views between the positional features of protein and nucleic acid sequences and their 3D structures, providing researchers with a better understanding of the mechanisms underlying the functions of biological macromolecules at the atomic level.

BIOINFORMATICS (2022)

Review Biochemistry & Molecular Biology

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

John D. Westbrook et al.

Summary: PDBx/mmCIF is a data standard for structural biology, used for storing and disseminating three-dimensional structures of biological macromolecules. Developed collaboratively over three decades, involving contributions from multiple scientific disciplines, it accelerates the pace of scientific discovery.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Pharmacology & Pharmacy

Novel phthalimides regulating PD-1/PD-L1 interaction as potential immunotherapy agents

Chengliang Sun et al.

Summary: Programmed cell death 1 (PD-1)/programmed cell death ligand 1 (PD-L1) have emerged as promising immune checkpoint targets for cancer immunotherapy. This study focuses on the development of small-molecule inhibitors with improved binding capacity to PD-L1 protein. A novel phthalimide derivative, P39, was identified as the best inhibitor, which not only inhibited PD-1/PD-L1 interaction but also enhanced the killing efficacy of immune cells on cancer cells. P39 exhibited favorable safety profiles and showed significant in vivo antitumor activity through promoting CD8+ T cell activation.

ACTA PHARMACEUTICA SINICA B (2022)

Article Biochemistry & Molecular Biology

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level

Chenghua Shao et al.

Summary: This study analyzed the agreement between 3D atomic coordinates and experimental data in PDB MX structures, providing a metric for evaluating structure quality.

STRUCTURE (2022)

Review Biochemistry & Molecular Biology

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

Stephen K. Burley et al.

Summary: RCSB PDB, funded by multiple US agencies, is a global support center for structural biologists and PDB data users. It serves as the US data center and archive keeper for the worldwide PDB, providing storage and updating services. RCSB PDB serves thousands of depositors annually and offers free data access and education resources to millions of users worldwide.

BIOMOLECULES (2022)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K. Burley et al.

Summary: RCSB PDB, as the US data center for the global PDB archive, provides free access to 3D macromolecular structure data for millions of users worldwide, including educators, students, and the general public, integrating over 40 external biodata resources. The redesigned website now features improved search functionality and easier access to PDB data, showcasing new structures relevant to the understanding and addressing of the COVID-19 pandemic.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (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

An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19

Dafydd R. Owen et al.

Summary: PF-07321332, an orally bioavailable SARS-CoV-2 main protease inhibitor, has been discovered with in vitro pan-human coronavirus antiviral activity and excellent off-target selectivity and in vivo safety profiles. This new drug has shown promise in countering the threat of COVID-19 with its oral activity and safety in clinical trials.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

Zukang Feng et al.

Summary: The worldwide Protein Data Bank has collaborated with Global Phasing Ltd. and the Noguchi Institute to enhance validation reports for small molecules, including 2D diagrams and 3D electron density maps, to improve confidence in ligand conformation and interactions with macromolecules.

STRUCTURE (2021)

Article Multidisciplinary Sciences

Checkpoint inhibition through small molecule-induced internalization of programmed death-ligand 1

Jang-June Park et al.

Summary: A mechanism of inhibiting programmed death-ligand 1 through small molecule-induced dimerization and internalization was reported, showing potential therapeutic implications in oncology and chronic viral infections.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

New system for archiving integrative structures

Brinda Vallat et al.

Summary: Structures of complex biological assemblies are increasingly determined using integrative approaches and archived in the PDB-Dev system, which ensures that the data is findable, accessible, interoperable, and reusable for everyone.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Yana Rose et al.

Summary: RCSB PDB serves millions of users worldwide with experimentally determined 3D structures of biomolecules, delivering data efficiently through new APIs and a search system that integrates heterogeneous types of searches. The new architecture adheres to FAIR Principles, empowering users to address a wide array of research problems in fundamental biology and biomedicine.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal et al.

Summary: Large biomolecular structures are being determined experimentally using established techniques such as crystallography and electron microscopy, with performance requirements for visualization and analysis tools increasing rapidly. The Mol* Viewer is an advanced online web-native 3D visualization tool that allows visualization of complex structures, and is the primary tool used by PDBe and RCSB PDB.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction

Stephen K. Burley et al.

Summary: Established in 1971, the Protein Data Bank (PDB) serves as a public good by providing open access to over 175,000 experimentally determined structures of proteins, nucleic acids, and their complexes. Users from various fields benefit from the wealth of 3D structure data stored in the PDB, which has led to significant advances in protein structure prediction using artificial intelligence and machine learning methods.

STRUCTURE (2021)

Article Chemistry, Medicinal

Design, Synthesis, and Biological Evaluation of Imidazopyridines as PD-1/PD-L1 Antagonists

Roberto Butera et al.

Summary: In this study, a new scaffold based on high-resolution structures was designed, leading to the development of a class of potential PD-L1 antagonists. These compounds showed strong affinity for PD-L1 through biological activity testing, providing a potential avenue for the development of novel PD-L1 antagonists.

ACS MEDICINAL CHEMISTRY LETTERS (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

Review Biochemistry & Molecular Biology

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development

Stephen K. Burley

Summary: The Protein Data Bank (PDB) is a crucial international data resource storing experimentally determined atomic structures of proteins and nucleic acids. The information is essential for research and education, with biomedical researchers being the primary users. These structures are used for validating drug targets, guiding medicinal chemistry optimization, and other applications in academia and industry.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

PubChem in 2021: new data content and improved web interfaces

Sunghwan Kim et al.

Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Thera-SAbDab: the Therapeutic Structural Antibody Database

Matthew I. J. Raybould et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

David S. Goodsell et al.

PROTEIN SCIENCE (2020)

Review Pharmacology & Pharmacy

Impact of the Protein Data Bank on antineoplastic approvals

John D. Westbrook et al.

DRUG DISCOVERY TODAY (2020)

Article Multidisciplinary Sciences

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Zhenming Jin et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Insights from 20 years of the Molecule of the Month

David S. Goodsell et al.

BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION (2020)

Letter Biochemical Research Methods

The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences

Issaku Yamada et al.

NATURE METHODS (2020)

Article Biochemistry & Molecular Biology

Integrative illustration for coronavirus outreach

David S. Goodsell et al.

PLOS BIOLOGY (2020)

Article Multidisciplinary Sciences

Atomic-resolution protein structure determination by cryo-EM

Ka Man Yip et al.

NATURE (2020)

Article Multidisciplinary Sciences

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Francois Aguet et al.

SCIENCE (2020)

Article Biochemical Research Methods

RCSB Protein Data Bank 1D tools and services

Joan Segura et al.

BIOINFORMATICS (2020)

Letter Biochemistry & Molecular Biology

GlyGen: Computational and Informatics Resources for Glycoscience

William S. York et al.

GLYCOBIOLOGY (2020)

Article Chemistry, Medicinal

Fragment-based screening of programmed death ligand 1 (PD-L1)

Evan Perry et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2019)

Article Biochemical Research Methods

BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Archiving and disseminating integrative structure models

Brinda Vallat et al.

JOURNAL OF BIOMOLECULAR NMR (2019)

Article Biochemistry & Molecular Biology

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

Jeffrey R. Wagner et al.

STRUCTURE (2019)

Article Chemistry, Medicinal

Comparative Assessment of Scoring Functions: The CASF-2016 Update

Minyi Su et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Biochemistry & Molecular Biology

Protein Data Bank: the single global archive for 3D macromolecular structure data

Stephen K. Burley et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

SCOPe: classification of large macromolecular structures in the structural classification of proteinsextended database

John-Marc Chandonia et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

Thomas D. Newport et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

John D. Westbrook et al.

STRUCTURE (2019)

Article Biochemistry & Molecular Biology

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Helen M. Berman et al.

STRUCTURE (2019)

Article Biochemistry & Molecular Biology

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

Antonio J. M. Ribeiro et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

Jurgen Haas et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)

Article Mathematical & Computational Biology

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y. Young et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)

Article Multidisciplinary Sciences

Analysis of impact metrics for the Protein Data Bank

Christopher Markosian et al.

SCIENTIFIC DATA (2018)

Article Multidisciplinary Sciences

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Chenghua Shao et al.

SCIENTIFIC DATA (2018)

Article Biochemistry & Molecular Biology

Pharos: Collating protein information to shed light on the druggable genome

Dac-Trung Nguyen et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

The ChEMBL database in 2017

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

GlyTouCan: an accessible glycan structure repository

Michael Tiemeyer et al.

GLYCOBIOLOGY (2017)

Letter Multidisciplinary Sciences

A global coalition to sustain core data

Warwick P. Anderson

NATURE (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 Pharmacology & Pharmacy

Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities

Jennifer M. Beierlein et al.

CLINICAL THERAPEUTICS (2017)

Article Biochemistry & Molecular Biology

PDBFlex: exploring flexibility in protein structures

Thomas Hrabe et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

EMDataBank unified data resource for 3DEM

Catherine L. Lawson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

Michael K. Gilson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The Pfam protein families database: towards a more sustainable future

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Multidisciplinary

The Cambridge Structural Database

Colin R. Groom et al.

ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS (2016)

Article Chemistry, Multidisciplinary

DCC: a Swiss army knife for structure factor analysis and validation

Huanwang Yang et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2016)

Article Biochemistry & Molecular Biology

Manual classification strategies in the ECOD database

Hua Cheng et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1

Krzysztof M. Zak et al.

STRUCTURE (2015)

Article Biochemical Research Methods

Detection of circular permutations within protein structures using CE-CP

Spencer E. Bliven et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures

Aqeel Ahmed et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

IMGT®, the international ImMunoGeneTics information system® 25 years on

Marie-Paule Lefranc et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

The immune epitope database (IEDB) 3.0

Randi Vita et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

SCOP2 prototype: a new approach to protein structure mining

Antonina Andreeva et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

SAbDab: the structural antibody database

James Dunbar et al.

NUCLEIC ACIDS RESEARCH (2014)

Editorial Material Biology

Collaboration gets the most out of software

Andrew Morin et al.

Article Biochemistry & Molecular Biology

GENCODE: The reference human genome annotation for The ENCODE Project

Jennifer Harrow et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

ExplorEnz: the primary source of the IUBMB enzyme list

Andrew G. McDonald et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemical Research Methods

Representation of viruses in the remediated PDB archive

Catherine L. Lawson et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

BioMagResBank

Eldon L. Ulrich et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Remediation of the protein data bank archive

Kim Henrick et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemical Research Methods

OPM: Orientations of proteins in membranes database

MA Lomize et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

RECOORD:: A recalculated coordinate database of 500+proteins from the PDB using restraints from the BioMagResBank

AJ Nederveen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

TM-align: a protein structure alignment algorithm based on the TM-score

Y Zhang et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemical Research Methods

Ligand Depot: a data warehouse for ligands bound to macromolecules

ZK Feng et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

FATCAT: a web server for flexible structure comparison and structure similarity searching

YZ Ye et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

Transmembrane proteins in the Protein Data Bank:: identification and classification

GE Tusnády et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

The RESID database of protein modifications as a resource and annotation tool

JS Garavelli

PROTEOMICS (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)

Letter Biochemistry & Molecular Biology

Announcing the worldwide Protein Data Bank

H Berman et al.

NATURE STRUCTURAL BIOLOGY (2003)

Article Biochemical Research Methods

STAR/mmCIF: An ontology for macromolecular structure

JD Westbrook et al.

BIOINFORMATICS (2000)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemistry & Molecular Biology

Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair

RZ Kramer et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)