Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods

Structural basis for antibody inhibition of flavivirus NS1–triggered endothelial dysfunction

(2021) Scott B. Biering et al.   SCIENCE

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

(2021) David Sehnal et al.   NUCLEIC ACIDS RESEARCH

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis

(2020) Lian-Mei Tan et al.   PLANT CELL

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

(2020) Zhichao Miao et al.   RNA

Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease

(2020) Lifeng Fu et al.   Nature Communications

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

(2019) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

CASP13 target classification into tertiary structure prediction categories

(2019) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction

(2019) Jun Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Assessment of protein assembly prediction in CASP13

(2019) Dmytro Guzenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Introducing “best single template” models as Reference Baseline for the Continuous Automated Model EvaluatiOn (CAMEO)

(2019) Juergen Haas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2019) Jeffrey R. Wagner et al.   STRUCTURE

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2017) Jürgen Haas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

(2017) Martino Bertoni et al.   Scientific Reports

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

(2016) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

iFoldRNA v2: folding RNA with constraints: Fig. 1.

(2015) Andrey Krokhotin et al.   BIOINFORMATICS

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes

(2014) Kliment Olechnovič et al.   NUCLEIC ACIDS RESEARCH

OpenStructure: an integrated software framework for computational structural biology

(2013) M. Biasini et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP9 target classification

(2011) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH