PROFEAT
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Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.
Description
More detailed information about this field from each metasource.
Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
Webpage:
http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgiWebpage
More detailed information about this field from each metasource.
http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
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Name: UnlicenseLicence name
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Publications:
Publications
More detailed information about this field from each metasource.
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PMID: 16845018
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PMID: 21609959
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks
PMID: 27742592
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
Publications
More detailed information about this field from each metasource.
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PMID: 16845018
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PMID: 21609959
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks
PMID: 27742592
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
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PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PubMed citations: 80.
80 articles citing: PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. PMID:35296652
Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts. PMID:35283858
SCORPION is a stacking-based ensemble learning framework for accurate prediction of phage virion proteins. PMID:35260777
Large-scale comparative review and assessment of computational methods for phage virion proteins identification. PMID:35145365
ILeukin10Pred: A Computational Approach for Predicting IL-10-Inducing Immunosuppressive Peptides Using Combinations of Amino Acid Global Features. PMID:35053004
MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors. PMID:34750626
Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor. PMID:34649499
Deep Learning for Protein-Protein Interaction Site Prediction. PMID:34236667
Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs. PMID:34202954
Discovery of Novel eEF2K Inhibitors Using HTS Fingerprint Generated from Predicted Profiling of Compound-Protein Interactions. PMID:34065377
Analysis of protein determinants of host-specific infection properties of polyomaviruses using machine learning. PMID:33646531
Identification of Stress-Related Genes and a Comparative Analysis of the Amino Acid Compositions of Translated Coding Sequences Based on Draft Genome Sequences of Antarctic Yeasts. PMID:33633709
DTI-SNNFRA: Drug-target interaction prediction by shared nearest neighbors and fuzzy-rough approximation. PMID:33606741
LPI-SKF: Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions. PMID:33362868
Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. PMID:33316035
ISLAND: in-silico proteins binding affinity prediction using sequence information. PMID:33292419
Better understanding and prediction of antiviral peptides through primary and secondary structure feature importance. PMID:33159146
Predicting Drug-Target Interactions with Electrotopological State Fingerprints and Amphiphilic Pseudo Amino Acid Composition. PMID:32784497
Protein-Protein Interactions Efficiently Modeled by Residue Cluster Classes. PMID:32640745
An automatic representation of peptides for effective antimicrobial activity classification. PMID:32180904
Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods. PMID:32153730
Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks. PMID:31874614
RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. PMID:31802128
An in silico Approach for Integrating Phenotypic and Target-based Approaches in Drug Discovery. PMID:31638744
Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins. PMID:31387337
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information. PMID:31123959
Machine learning antimicrobial peptide sequences: Some surprising variations on the theme of amphiphilic assembly. PMID:31093008
Revealing Drug-Target Interactions with Computational Models and Algorithms. PMID:31052598
3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. PMID:30108817
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. PMID:29528364
CIPPN: computational identification of protein pupylation sites by using neural network. PMID:29312575
What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning? PMID:29147555
UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences. PMID:29135934
Machine learning-enabled discovery and design of membrane-active peptides. PMID:28728899
Drug-target interaction prediction via class imbalance-aware ensemble learning. PMID:28155697
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
Roles of d-Amino Acids on the Bioactivity of Host Defense Peptides. PMID:27376281
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
Prediction of Protein Submitochondrial Locations by Incorporating Dipeptide Composition into Chou's General Pseudo Amino Acid Composition. PMID:26746980
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. PMID:25982853
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. PMID:25705262
A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach. PMID:25527073
Predicting host tropism of influenza A virus proteins using random forest. PMID:25521718
How do eubacterial organisms manage aggregation-prone proteome? PMID:25339987
A novel feature extraction scheme with ensemble coding for protein-protein interaction prediction. PMID:25046746
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. PMID:24952641
A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli. PMID:24885721
An ensemble method approach to investigate kinase-specific phosphorylation sites. PMID:24872686
Computational chemogenomics: is it more than inductive transfer? PMID:24771144
Application of Hybrid Functional Groups to Predict ATP Binding Proteins. PMID:24729962
SPiCE: a web-based tool for sequence-based protein classification and exploration. PMID:24685258
Multi-algorithm and multi-model based drug target prediction and web server. PMID:24487966
Structural determinants for protein adsorption/non-adsorption to silica surface. PMID:24282583
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. PMID:24059743
Prediction of lung tumor types based on protein attributes by machine learning algorithms. PMID:23888262
A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms. PMID:23799117
The development of a universal in silico predictor of protein-protein interactions. PMID:23741499
Improved classification of lung cancer tumors based on structural and physicochemical properties of proteins using data mining models. PMID:23505559
An ensemble method for predicting subnuclear localizations from primary protein structures. PMID:23460833
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. PMID:23283513
CyanoPhyChe: a database for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins. PMID:23185330
Classification of lung cancer tumors based on structural and physicochemical properties of proteins by bioinformatics models. PMID:22829872
A systematic prediction of multiple drug-target interactions from chemical, genomic, and pharmacological data. PMID:22666371
Exploiting heterogeneous features to improve in silico prediction of peptide status - amyloidogenic or non-amyloidogenic. PMID:22373069
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. PMID:21609959
Analysis of multiple compound-protein interactions reveals novel bioactive molecules. PMID:21364574
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins. PMID:21235786
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. PMID:21127034
An improved classification of G-protein-coupled receptors using sequence-derived features. PMID:20696050
Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. PMID:20569422
Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines. PMID:20066123
CAMP: a useful resource for research on antimicrobial peptides. PMID:19923233
Enzyme classification with peptide programs: a comparative study. PMID:19630945
A chemogenomics view on protein-ligand spaces. PMID:19534738
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides. PMID:18294399
Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding. PMID:17967170
Efficacy of different protein descriptors in predicting protein functional families. PMID:17705863 -
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
PubMed citations: 35.
35 articles citing: Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions. PMID:35298816
Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts. PMID:35283858
Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor. PMID:34649499
Protein music of enhanced musicality by music style guided exploration of diverse amino acid properties. PMID:34632134
Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. PMID:33995923
Identification of Stress-Related Genes and a Comparative Analysis of the Amino Acid Compositions of Translated Coding Sequences Based on Draft Genome Sequences of Antarctic Yeasts. PMID:33633709
Toward insights on determining factors for high activity in antimicrobial peptides via machine learning. PMID:31875156
Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides. PMID:30936317
Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target. PMID:30429792
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. PMID:30285084
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification. PMID:29997509
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. PMID:29868903
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. PMID:29724166
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. PMID:29528364
CIPPN: computational identification of protein pupylation sites by using neural network. PMID:29312575
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. PMID:28732462
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. PMID:28334201
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. PMID:27307615
Crysalis: an integrated server for computational analysis and design of protein crystallization. PMID:26906024
PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2. PMID:26339154
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. PMID:25982853
PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection. PMID:25148528
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. PMID:24952641
Computational chemogenomics: is it more than inductive transfer? PMID:24771144
SPiCE: a web-based tool for sequence-based protein classification and exploration. PMID:24685258
PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations. PMID:24675610
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. PMID:24493033
Bagging with CTD--a novel signature for the hierarchical prediction of secreted protein trafficking in eukaryotes. PMID:24316328
Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics. PMID:24267406
Prediction of lung tumor types based on protein attributes by machine learning algorithms. PMID:23888262
Improved classification of lung cancer tumors based on structural and physicochemical properties of proteins using data mining models. PMID:23505559
An ensemble classifier for eukaryotic protein subcellular location prediction using gene ontology categories and amino acid hydrophobicity. PMID:22303481 -
PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks
PubMed citations: 16.
16 articles citing: PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks
Drug-target interaction prediction via multiple classification strategies. PMID:35057737
Computational Prediction of Compound-Protein Interactions for Orphan Targets Using CGBVS. PMID:34500569
Deep Learning for Protein-Protein Interaction Site Prediction. PMID:34236667
Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs. PMID:34202954
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. PMID:33995923
Predicting Drug-Target Interactions with Electrotopological State Fingerprints and Amphiphilic Pseudo Amino Acid Composition. PMID:32784497
PARGT: a software tool for predicting antimicrobial resistance in bacteria. PMID:32620856
Optimization of Inhibitory Peptides Targeting Phosphoprotein of Rabies Virus. PMID:32431572
Human body-fluid proteome: quantitative profiling and computational prediction. PMID:32020158
Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis. PMID:31806906
ProTstab - predictor for cellular protein stability. PMID:31684883
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. PMID:31045209
mACPpred: A Support Vector Machine-Based Meta-Predictor for Identification of Anticancer Peptides. PMID:31013619
Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target. PMID:30429792
Tags:
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More detailed information about this field from each metasource.
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
protein structural motifs and surfaces
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
protein sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.745999
Tags
More detailed information about this field from each metasource.
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
protein structural motifs and surfaces
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
protein sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:31.745999
small molecule protein interaction protein structural motifs and surfaces protein sites, features and motifs structure prediction
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