Continuously Automated Model Evaluation
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Continuously Automated Model Evaluation
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
CAMEO
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Continuously Automated Model Evaluation
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
CAMEO
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Continuously Automated Model Evaluation
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
CAMEO
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development.
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Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development.
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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http://cameo3d.org/Webpage
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http://cameo3d.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Name: CAMEO Terms and Conditions of UseLicence name
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CAMEO Terms and Conditions of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
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http://cameo3d.org/cameong_terms/
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
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The Protein Model Portal--a comprehensive resource for protein structure and model information
PMID: 23624946
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
The Protein Model Portal--a comprehensive resource for protein structure and model information
PMID: 23624946
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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The Protein Model Portal--a comprehensive resource for protein structure and model information
PubMed citations: 138.
138 articles citing: The Protein Model Portal--a comprehensive resource for protein structure and model information
Deep learning geometrical potential for high-accuracy ab initio protein structure prediction. PMID:35663033
A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models. PMID:35324806
Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential. PMID:35139120
Secondary structure specific simpler prediction models for protein backbone angles. PMID:34983370
New system for archiving integrative structures. PMID:34866606
The AlphaFold Database of Protein Structures: A Biologist's Guide. PMID:34757056
Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. PMID:34702851
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. PMID:34137435
Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14. PMID:34035363
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PMID:33770072
Improved Protein Model Quality Assessment By Integrating Sequential And Pairwise Features Using Deep Learning. PMID:33325480
Enhancing protein backbone angle prediction by using simpler models of deep neural networks. PMID:33173130
Predicting binding sites from unbound versus bound protein structures. PMID:32985584
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Dark Proteome Database: Studies on Disorder. PMID:32629790
Protein Contact Map Prediction Based on ResNet and DenseNet. PMID:32337273
Machine Learning Approaches for Quality Assessment of Protein Structures. PMID:32316682
Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PMID:32295225
Immunoinformatics and Vaccine Development: An Overview. PMID:32161726
Exploring the computational methods for protein-ligand binding site prediction. PMID:32140203
SGID: a comprehensive and interactive database of the silkworm. PMID:31836898
Molecular replacement using structure predictions from databases. PMID:31793899
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). PMID:31633216
The association between TNP2 gene polymorphisms and Iranian infertile men with varicocele: A case-control study. PMID:31583373
Improved homology modeling of the human & rat EP4 prostanoid receptors. PMID:31455205
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. PMID:31427836
A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation. PMID:31401411
Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13. PMID:31292988
Arming oHSV with ULBP3 drives abscopal immunity in lymphocyte-depleted glioblastoma. PMID:31292299
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
The Selective Rat Toxicant Norbormide Blocks KATP Channels in Smooth Muscle Cells But Not in Insulin-Secreting Cells. PMID:31191321
Principles for Integrative Structural Biology Studies. PMID:31150619
Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes. PMID:31148576
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
Dark Proteome Database: Studies on Dark Proteins. PMID:30934744
Anticipating innovations in structural biology. PMID:30912485
Protein structure prediction. PMID:30853739
Small Molecule Docking of DNA Repair Proteins Associated with Cancer Survival Following PCNA Metagene Adjustment: A Potential Novel Class of Repair Inhibitors. PMID:30759820
Privileged Structures and Polypharmacology within and between Protein Families. PMID:30613326
Protein structure networks provide insight into active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis. PMID:30516771
Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. PMID:30375376
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. PMID:30239678
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. PMID:30109435
A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. PMID:30087916
PredMP: a web server for de novo prediction and visualization of membrane proteins. PMID:30084960
Molecular docking and pharmacological/toxicological assessment of a new compound designed from celecoxib and paracetamol by molecular hybridization. PMID:30039481
Transcriptional and Translational Landscape of Equine Torovirus. PMID:29950409
Electrostatic Tuning of a Potassium Channel in Electric Fish. PMID:29937349
Protein alignment based on higher order conditional random fields for template-based modeling. PMID:29856860
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. PMID:29846643
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. PMID:29796670
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
The first case of NSHL by direct impression on EYA1 gene and identification of one novel mutation in MYO7A in the Iranian families. PMID:29511501
Protein homology model refinement by large-scale energy optimization. PMID:29507254
Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks. PMID:29275173
Computational Studies of Snake Venom Toxins. PMID:29271884
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. PMID:29206185
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12. PMID:29178137
LIBRA-WA: a web application for ligand binding site detection and protein function recognition. PMID:29126218
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
The NSAID allosteric site of human cytosolic sulfotransferases. PMID:29038294
Guidelines for the use of flow cytometry and cell sorting in immunological studies. PMID:29023707
Folding Membrane Proteins by Deep Transfer Learning. PMID:28957654
Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. PMID:28913931
Antiproliferative factor (APF) binds specifically to sites within the cytoskeleton-associated protein 4 (CKAP4) extracellular domain. PMID:28893174
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling. PMID:28884168
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. PMID:28874689
Analysis of deep learning methods for blind protein contact prediction in CASP12. PMID:28845538
Bradyrhizobium elkanii nod regulon: insights through genomic analysis. PMID:28767122
The Dark Proteome Database. PMID:28736578
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models. PMID:28460136
WDR23 regulates NRF2 independently of KEAP1. PMID:28453520
GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. PMID:28387820
Comparing co-evolution methods and their application to template-free protein structure prediction. PMID:28171606
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. PMID:28150250
Protein Bioinformatics Databases and Resources. PMID:28150231
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PMID:28056090
Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis. PMID:28040565
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. PMID:28035027
Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. PMID:27991516
Replication Protein A Presents Canonical Functions and Is Also Involved in the Differentiation Capacity of Trypanosoma cruzi. PMID:27984589
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
PRIMO: An Interactive Homology Modeling Pipeline. PMID:27855192
Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. PMID:27796781
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. PMID:27766851
ProQ3: Improved model quality assessments using Rosetta energy terms. PMID:27698390
A Novel Role for Progesterone Receptor Membrane Component 1 (PGRMC1): A Partner and Regulator of Ferrochelatase. PMID:27599036
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. PMID:27587688
Pharmacological targeting of the PDGF-CC signaling pathway for blood-brain barrier restoration in neurological disorders. PMID:27524729
Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms. PMID:27513851
The archiving and dissemination of biological structure data. PMID:27450113
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. PMID:27378301
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. PMID:27307635
Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking. PMID:27242194
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. PMID:27190006
Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models. PMID:27149620
CoinFold: a web server for protein contact prediction and contact-assisted protein folding. PMID:27112569
Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes. PMID:27040368
MreB-Dependent Organization of the E. coli Cytoplasmic Membrane Controls Membrane Protein Diffusion. PMID:26958890
The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response. PMID:26863566
ProQ2: estimation of model accuracy implemented in Rosetta. PMID:26733453
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
Protein Structure and Function Prediction Using I-TASSER. PMID:26678386
Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. PMID:26677056
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Unexpected features of the dark proteome. PMID:26578815
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. PMID:26545824
MECP2 missense mutations outside the canonical MBD and TRD domains in males with intellectual disability. PMID:26490184
Antisera Against Certain Conserved Surface-Exposed Peptides of Nontypeable Haemophilus influenzae Are Protective. PMID:26390432
ABCB4 mutations in adult patients with cholestatic liver disease: impact and phenotypic expression. PMID:26324191
Dynamic profiling of double-stranded RNA binding proteins. PMID:26184879
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. PMID:26095030
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Novel Drug Targets for Food-Borne Pathogen Campylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study. PMID:26061459
RBO Aleph: leveraging novel information sources for protein structure prediction. PMID:25897112
I-TASSER server: new development for protein structure and function predictions. PMID:25883148
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. PMID:25820431
Discovery of novel new Delhi metallo-β-lactamases-1 inhibitors by multistep virtual screening. PMID:25734558
Data to knowledge: how to get meaning from your result. PMID:25610627
The I-TASSER Suite: protein structure and function prediction. PMID:25549265
C-Terminally fused affinity Strep-tag II is removed by proteolysis from recombinant human erythropoietin expressed in transgenic tobacco plants. PMID:25504272
Protein structure annotation resources. PMID:25502191
A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. PMID:25461536
Antifreeze proteins enable plants to survive in freezing conditions. PMID:25431421
Uncertainty in integrative structural modeling. PMID:25173450
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). PMID:25161240
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. PMID:24782522
An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation. PMID:24365473
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
Protein modeling: what happened to the "protein structure gap"? PMID:24010712
Comparative protein structure modeling using Modeller. PMID:18428767
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benchmarking
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
crowdsourcing
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Tags
More detailed information about this field from each metasource.
benchmarking
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
crowdsourcing
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
experimental measurement
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: CAMEO; Continuously Automated Model Evaluation; DOI: https://doi.org/10.25504/FAIRsharing.dq34p2; Last edited: Jan. 3, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
benchmarking computational predictions crowdsourcing experimental measurement mathematical model protein protein structure
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