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290
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Databases/Tools
NAR database/Web Server and OBRC
The PredictProtein server
Predict protein structure and function based on protein sequence.
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AggreProt: a web server for predicting and engineering aggregation prone regions in proteins.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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DOMAC -- a hybrid protein domain prediction server
An accurate protein domain prediction server.
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CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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The MPI Bioinformatics Toolkit for protein sequence analysis
Conduct protein sequence and structure analysis using a suite of software tools.
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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.
Nucleic Acids Res. 2024 Jul 05;52(W1)
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Protein structure prediction servers at University College London
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PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks.
Nucleic Acids Res. 2023 Jul 05;51(W1)
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EVA -- evaluation of protein structure prediction servers
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InterPro in 2022.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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Integrated databanks access and sequence/structure analysis services at the PBIL
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TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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The Yeast Resource Center Public Data Repository
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HProteome-BSite: predicted binding sites and ligands in human 3D proteome.
Nucleic Acids Res. 2023 Jan 06;51(D1)
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PROSPECT-PSPP -- An automatic computational pipeline for protein structure prediction
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DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.
Nucleic Acids Res. 2022 Jul 05;50(W1)
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PROTEUS2 -- a web server for comprehensive protein structure prediction and structure-based annotation
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LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.
Nucleic Acids Res. 2022 Jul 05;50(W1)
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PROTINFO -- new algorithms for enhanced protein structure predictions
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dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.
Nucleic Acids Res. 2022 Jan 07;50(D1)
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Pcons.net -- protein structure prediction meta server
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DeepRefiner: high-accuracy protein structure refinement by deep network calibration.
Nucleic Acids Res. 2021 Jul 02;49(W1)
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Robetta Server -- Protein structure prediction and analysis
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AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.
Nucleic Acids Res. 2020 Jul 02;48(W1)
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SAM-T08 -- HMM-based Protein Structure Prediction
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LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.
Nucleic Acids Res. 2019 Jul 02;47(W1)
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(PS)2 -- Protein Structure Prediction Server
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Res. 2018 Jul 02;46(W1)
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GeneSilico protein structure prediction meta-server
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GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.
Nucleic Acids Res. 2017 Jul 03;45(W1)
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META-PP -- single interface to crucial prediction servers
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(PS)2: protein structure prediction server version 3.0.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes
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RBO Aleph: leveraging novel information sources for protein structure prediction.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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Decoys 'R' Us
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I-TASSER server: new development for protein structure and function predictions.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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VADAR -- a web server for quantitative evaluation of protein structure quality
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IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
Nucleic Acids Res. 2015 Jul 01;43(W1)
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The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
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BPROMPT -- a consensus server for membrane protein prediction
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BCM Search Launcher
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NCI -- a server to identify non-canonical interactions in protein structures
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BOMP -- A Program to Predict Integral xdf-barrel Outer Membrane Proteins Encoded within Genomes of Gram-negative Bacteria
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DSSPcont -- continuous secondary structure assignments for proteins
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ESPript/ENDscript -- extracting and rendering sequence and 3D information from atomic structures of proteins
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EVAcon -- a protein contact prediction evaluation service
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GTOP -- Genomes to Protein structures and functions database
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Geno3D -- Protein Modeling Tool
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GlobPlot -- exploring protein sequences for globularity and disorder
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I-TASSER: Protein Structure & Function Predictions
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Localizome -- a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
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PEP-FOLD -- De Novo Peptide Structure Prediction
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PONGO -- a web server for multiple predictions of all-alpha transmembrane proteins
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PRED-TMBB -- A Web Server for Predicting the Topology of xdf-barrel Outer Membrane Proteins
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PatchDock and SymmDock -- servers for rigid and symmetric docking
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ProTarget -- automatic prediction of protein structure novelty
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QMEAN -- Server for Model Quality Estimation
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SAHG -- Structural Atlas of the Human Genome
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SCRATCH -- a protein structure and structural feature prediction server
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SPROUTS -- Structural Prediction for Protein Folding Utility System
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SWISS-MODEL -- an automated protein homology-modeling server
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Scooby-domain -- prediction of globular domains in protein sequence
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TRAMPLE -- the transmembrane protein labeling environment
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The HHpred interactive server for protein homology detection and structure prediction
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The Jpred 3 secondary structure prediction server
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Tools for comparative protein structure modeling and analysis
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wwLigCSRre -- Ligand-based Screening server
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Find More Resources from PubMed Articles
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free
protein structure prediction
.
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Journal:
BMC Bioinformatics. 2019 Apr 25;20(1)
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End-to-End Differentiable Learning of Protein Structure.
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Cell Syst. 2019 Apr 24;8(4)
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Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13.
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Proteins. 2019 Dec;87(12)
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DESTINI: A deep-learning approach to contact-driven
protein structure prediction
.
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Journal:
Sci Rep. 2019 Mar 05;9(1)
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Graph-Based Community Detection for Decoy Selection in Template-Free
Protein Structure Prediction
.
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Journal:
Molecules. 2019 Feb 28;24(5)
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Protein structure prediction
from inaccurate and sparse NMR data using an enhanced genetic algorithm.
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Journal:
Comput Biol Chem. 2019 Apr;79
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Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.
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Bioinformatics. 2019 Jul 15;35(14)
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BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution.
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Comput Biol Med. 2019 Jan;104
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Two New Heuristic Methods for Protein Model Quality Assessment.
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Journal:
IEEE/ACM Trans Comput Biol Bioinform. 2020;17(4)
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Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning.
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Journal:
J Comput Chem. 2018 Oct 05;39(26)
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Topic Clusters
remix
Top
717
Results
+
Deep learning
(90)
+
Fold
(61)
+
Algorithm
(72)
+
Neural networks
(52)
+
Machine
(48)
+
Analysis
(30)
+
Residue
(50)
+
Alignment, Multiple sequence
(27)
+
Model quality
(27)
+
De novo
(23)
+
Ligand, Binding Sites
(14)
+
Computational
(11)
+
Knowledge-based
(25)
+
Secondary structure
(18)
+
Free
(15)
+
Helix, Transmembrane
(13)
+
Application
(18)
+
Ab Initio
(20)
+
Template-based
(21)
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Docking
(13)
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