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Peptides, antibodies, epitopes

 

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SPRINT Sequence-based prediction of protein-peptide binding sites using support vector machine online
pepATTRACT Peptide-protein docking online
CPPred-RF Predictor cell-penetrating peptides online
PIGSPro Prediction of Ab structures online
SATPdb A database of structurally annotated therapeutic peptides online
PeptiDock ClusPro PeptiDock (Efficient global docking of peptide recognition motifs using FFT) online
ACCLUSTER Peptide Binding Site Prediction online
Smiles2Monomers Smiles2Monomers is a server to infer monomeric structure of polymers from their atomic structure online
PEPstrMOD Predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues online
APD3 The antimicrobial peptide database as a tool for research and education online
TepiTool A Pipeline for Computational Prediction of T Cell Epitope Candidates online
Peptiderive Derive peptide inhibitors from protein–protein interactions online
C2Pred Prediction of cell penetrating peptides with feature selection techniques online
Antibody The Antibody Registry was created to give researchers a way to universally identify antibodies used in in the course of their research online
AbMiner AbMiner is a tool that allows users to search for appropriate, commercially available antibodies for research purposes online
Antibodypedia An open-access database of publicly available antibodies against human protein targets online
Monoclonal Monoclonal antibody index online
mCSM-AB A server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures online
MoRFchibi Tools for the identification of MoRFs (short segments within longer disordered protein regions that bind to globular protein domains in a process known as disorder-to-order transition) in protein sequences (2016) online
PEP-FOLD3 Faster de novo structure prediction for linear peptides in solution and in complex online
SAbPred A structure-based antibody prediction server online
PinaColada Design of protein-protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides are natural candidates for inhibition of protein-protein complexes. PinaColada, a novel computational method for the design of peptide inhibitors for protein-protein interactions (2016) online
PepComposer Computational design of peptides binding to a given protein surface online
CoinFold Protein contact prediction and contact-assisted protein folding (input sequence) online
PhyreStorm A Web Server for Fast Structural Searches Against the PDB (can help for peptides) online
dPABBs A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides online
THPdb A database of FDA approved therapeutic peptides and proteins online
LEADS-PEP 53 protein-peptide complexes with peptide lengths ranging from 3 to 12 residues. A Benchmark Data Set for Assessment of Peptide Docking Performance database
TAGSFREE Design split-and-mix peptide libraries standalone
EPI-peptide EPI-peptide designer: a tool for designing peptide ligand libraries based on epitope–paratope interactions standalone
Helixem A place to design stapled peptides (vitro) online
iACP A sequence-based tool for identifying anticancer peptides (2016) online
Fit3D A bioinformatics web service to search for spatial residue patterns in proteins, so-called structural motifs online
AntiAngioPred A Server for Prediction of Anti-Angiogenic Peptides online
CleavPredict A platform for reasoning about proteolytic events online
AHTPDB A comprehensive platform for analysis and presentation of antihypertensive peptides (manually curated database) database
CAMPR3 A database on sequences, structures and signatures of antimicrobial peptides database
NNvPDB Neural Network based Protein Secondary Structure Prediction with PDB Validation (2015) online
CONFOLD Residue-residue contact-guided ab initio protein folding online
JPred4 A protein secondary structure prediction server (2015). Well known others with high accuracy are PSIPRED and PredictProtein online
PredictProtein An open resource for online prediction of protein structural and functional features (ppopen) online
QSPs Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication online
PyIgClassify A database of antibody CDR structural classifications online
Peptidecutter PeptideCutter predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence online
PROSPER PROSPER is an integrated feature-based webserver for in silico prediction of protease substrates and their cleavage sites for twenty-four different protease types, covering four major protease families- Aspartic (A), Cysteine (C), Metallo (M) and Serine (S) online
CutDB The CutDB focuses on the annotation of individual proteolytic events, both actual and predicted online
PMAP Databases for analyzing proteolytic events and pathways online
Appnn Prediction of Peptide and Protein Propensity for Amyloid Formation (Appnn: Amyloid Propensity Prediction Neural Network) (2015) online and standalone
pepATTRACT Peptide-Protein Docking with pepATTRACT (2015) online and standalone
Bio-AIMS Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models. Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins (2015) online
Epitome A database of all known antigenic residues and the antibodies that interact with them database
Epitopemap A web application for integrated whole proteome epitope prediction (2015) online and standalone
proABC A predictor of Antibody-Antigen interactions based on the Random Forest Algorithm online
EpiPred Improving B-cell epitope prediction and its application to global antibody-antigen docking presently standalone
EPMeta EPMeta: A Meta Server for Prediction of Antigenic Epitopes presently standalone
OptMAVEn A New Framework for the de novo Design of Antibody Variable Region Models Targeting Specific Antigen Epitopes standalone
antibody Antibody Structure Summary Page online
ABodyBuilder Antibody modeling online
SAbPred Antibody modelling tools and prediction software from the Oxford Protein Informatics Group (OPIG) online
antibody Immunological Databases and Tools online
iedb Epitope Prediction and Analysis Tools (with for instance Bepipred, Parker hydrophilicity, beta-turn prediction... Surface accessibility..) online
EpIC A rational pipeline for epitope immunogenicity characterization online
EPMLR Sequence-based linear B-cell epitope prediction method using multiple linear regression (protein sequence) online
APCpred Predicting linear B-cell epitopes using amino acid anchoring pair composition (protein sequence) online
BEpro Discontinuous B-cell epitope prediction (formerly PEPITO) online
PCSS Peptide Classification using Sequence and Structure online
DiscoTope Predicts discontinuous B cell epitopes from protein three dimensional structures. The method utilizes calculation of surface accessibility (estimated in terms of contact numbers) and a novel epitope propensity amino acid score online
Epitopia Server for detection of immunogenic regions in protein structures (need sequence info in the PDB file) or sequences online
PEASE Predicting Epitopes using Antibody Sequence online
EPSVR Antigenic Epitopes Prediction with Support Vector Regression online
EpiToolKit A Web-based Workbench for Vaccine Design datasets
IEDB Immune Epitope Database database
DIGIT A database of immunoglobulins with integrated tools database
Peptaibiotics The peptaibiotics database database
GalaxyPepDock A protein–peptide docking tool based on interaction similarity and energy optimization (2015) online
CATNAP CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research online
CABS-dock CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site online
BCSearch Fast structural fragment mining over large collections of protein structures online
SynLinker A tool for designing linkers and synthetic fusion proteins online
LinkerDB An analysis of protein domain linkers: their classification and role in protein folding online
WALTZ-DB A benchmark database of amyloidogenic hexapeptides database
Expitope A Web server for epitope expression. The tool enable the users to find all known proteins containing their peptide of interest. With this framework we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy (2015) online
peptiDB The Structural Basis of Peptide-Protein Binding Strategies. About 100 complexes indicated in the Supplement table datasets - list of PDB files
Proteax The Proteax module of iScienceSearch provides an easy way to perform substructure and structure similarity searches in major Internet databases containing peptides, such as PubChem, CheBI and ChemSpider starting from plain 3-letter-code peptide sequences commercial
DSDBASE A database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein database
protr/ProtrWeb R package and web server for generating various numerical representation schemes of protein sequences ProtrWeb, a user-friendly web server for calculating descriptors presented in the protr package (2015) online
PiPreD Knowledge-based modeling of peptides at protein interfaces (2014) online
FRAGRUS Knowledge-based sampling of protein backbone conformations for de novo structure-based protein design (2014) online
CancerPPD A database of anticancer peptides and proteins database
SwePep Sweden Peptide database database
TumorHoPe A Database of Tumor Homing Peptides (over 800 peptides in 2012) database
Peptides Peptides (anti cancer peptides, antibacterial peptides... from Raghava's group) database
Peptides Vaccine design in silico databases (from Raghava's group) database
AllerTOP A server for in silico prediction of allergens online
Tabhu Antibody humanization (Tabhu) a web server for antibody humanization online
Dynameomics Dynameomics Fragment Library: Fragment libraries were created to identify, rank and retrieve protein structure fragments from both the Dynameomics data warehouse and Protein Data Bank (PDB) for protein loop structure prediction online
FuzzyApp Fuzzy logic for personalized healthcare and diagnostics: a fuzzy logic based allergen-protein predictor online
AgAbDb Antigen-Antibody Interaction Database: a compendium of antigen-antibody interactions database
ADP The Antimicrobial Peptide Database (APD or APD2) contains 2429 antimicrobial peptides database
ParaPep A web resource for experimentally validated antiparasitic peptide sequences and their structures database
dbaasp Database of antimicrobial activity and structure of peptides database
HPVdb A data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology online
PFMFind A system for discovery of peptide homology and function standalone
Antibody i-Patch CDR contact prediction method. Antibody i-Patch works well with only the homology model of the antibody supplied as input standalone
Solubis Optimize your protein. Solubis plugin for YASARA standalone
BCL2DB Database of BCL-2 family members and BH3-only proteins database
HLP The web server HLP has been developed for assisting the scientific community for predicting intestinal half-life of peptides and to design mutant peptides with better half-life and physicochemical properties. HLP models were trained using a dataset of peptides whose half-lives have been determined experimentally in crude intestinal proteases preparation. Thus, HLP server will help in designing peptides possessing the potential to be administered via oral route online
Protein WISDOM The framework is divided into two stages: a sequence selection stage and a validation stage. The sequence selection stage designs novel protein and peptide sequences based upon a rigid or flexible design template uploaded by the user. Once sequence are generated, they can be validated by either fold specificity or approximate binding affinity. Fold specificity is a measure of how well the designed sequence adopts the template fold while approximate binding affinity is a measure of how well the designed sequence binds to a given protein target online
CPPsite CPPsite is a database of experimentally validated Cell Penetrating Peptides (10-30 amino acids) database
DoReMi Context-based prioritization of linear motif matches online
SEPPA 2.0 Server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen online
MoDPepInt An interactive webserver for prediction of modular domain-peptide interactions online
PASTA 2.0 An improved server for protein aggregation prediction online
Rosetta Rosettacommons, protocols to design oxopiperazine helix mimetics and other peptides for PPI online
PEP-SiteFinder A tool for the blind identification of peptide binding sites on protein surfaces online
NeuroPID NeuroPID: a classifier of neuropeptide precursors. Neuropeptides (NPs) are short secreted peptides produced in neurons online
AMPA An automated web server for prediction of protein antimicrobial regions (can be used to develop new peptide-based drugs against pathogens) online
Curie university of Texas EpiSearch: Automated Detection of Conformational Epitopes using Phage Display Peptide Sequences; BCEP: B-Cell Epitope Prediction Server; CrossReact: Web server to Predict Allergenic Protein Cross-reactivity online
ELM The eukaryotic linear motif resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs) .
MimoDB The MimoDB database can be used as a virtual control for phage display or any other surface display experiments. The peptide search tool is designed for this purpose to find out exact sequence matches. Experimental scientists can search their peptides against all peptides in the MimoDB database in batches to verify if each peptide has been reported by other groups with different targets. If so, that peptide may be a target-unrelated peptide rather than a true target binder database
DAMPD Dragon Antimicrobial Peptide Database database
American Peptide Company Peptides Commercial
Mimotopes Peptide company Commercial
Bachem Peptide company Commercial
Hemolytik Manually curated database of experimentally determined hemolytic and non-hemolytic peptides database
CAMP Collection of sequences and structures of antimicrobial peptides database
bNAbs The discovery of broadly neutralizing antibodies has provided an enormous impetus to the HIV vaccine research and to entire immunology. The bNAber database provides open, user-friendly access to detailed data on the rapidly growing list of HIV bNAbs, including neutralization profiles, sequences and three-dimensional structures (when available) database
SAbDab The structural antibody database database
AVPdb A database of experimentally validated antiviral peptides targeting medically important viruses database
PeptiSite A structural database of peptide binding sites in 4D database
CPPpred CPPpred: prediction of cell penetrating peptides online
AllergenFP Allergenicity Prediction by Descriptor Fingerprints online
MetAmyl A METa-Predictor for AMYLoid Proteins online
AMYPdb The amyloid protein database database and online tool
Fragger Protein fragment picker allowing to create and query protein fragment databases standalone
ToxinPred Helpful in predicting (i) toxicity or non-toxicity of peptides, (ii) minimum mutations in peptides for increasing or decreasing their toxicity, and (iii) toxic regions in proteins online
PepBind A Comprehensive Database and Computational Tool for Analysis of Protein-peptide Interactions database
Peptide Match The service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms online
IgBLAST An immunoglobulin variable domain sequence analysis tool online
BiDaS A web-based Monte Carlo BioData Simulator based on sequence/feature characteristics online
iELM Identification of short linear motif-mediated interfaces within the human interactome standalone
BlockLogo Visualization of peptide and sequence motif conservation online
Peptaibol Database of antimicrobial peptides database - peptide
LINK Defensins Knowledgebase It is a manually curated database and information source devoted to the defensin family of antimicrobial peptides database - peptide
PiHelper An open source framework for drug-target and antibody-target data standalone
LINK A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains online
VIOLIN The Vaccine Investigation and Online Information Network is a comprehensive vaccine database and analysis system. The VIOLIN database includes various types of vaccines and vaccine components. VIOLIN also includes Vaxign, a Web-based in silico vaccine design program based on the reverse vaccinology strategy online
SEPPA  Spatial Epitope Prediction of Protein Antigens server is a tool for conformational B-cell epitope prediction. With 3D protein structure as input, each residue in the query protein will be given a score according to its neighborhood residues' information. Higher score corresponds to higher probability the residue to be involved in an epitope. online
FOBIA FOlding By hIerarchical Assembly       online
IgBLAST An immunoglobulin variable domain sequence analysis tool online
LINK Some presumably non allergenic protein dataset can be obtained from Furmonaviciene and colleagues dataset
Aeroallergen Over 60 aeroallergen proteins can be found at the International union of immunological societies dataset
LINK 20 proteins aeroallergen proteins can be found at the SWISS-PROT Allergen Index dataset
ProtParam ExPASy Proteomics server-computational analysis of various physical and chemical parameters of proteins from its sequence dataset
AlgPred Prediction of Allergenic protein and mapping of IgE Epitopes dataset
Superficial  Approach to design peptide librairies that mimic the surface of a protein       online
VaccImm  Server that allows users to simulate peptide vaccination in cancer therapy. It uses an agent-based model that simulates peptide vaccination by explicitly modelling the involved cells (immune system and cancer) as well as molecules (antibodies, antigens and semiochemicals)       online
MSPeptider A web tool to predict the cross-section area of peptides from its primary sequence of amino acids       online
Quorumpeps  Database: chemical space, microbial origin and functionality of quorum sensing peptides       online
CrossTope A repository of 3D structures of immunogenic peptide: MHC complexes       online
CBS CBS Prediction Servers: numerous tools to analyze protein sequences, Post-translational modifications of proteins, Protein function and structure: BepiPred DiscoTope HLArestrictor NetChop NetCTL NetCTLpan NetMHC NetMHCcons NetMHCII NetMHCIIpan NetMHCpan NNAlign (Identifying sequence motifs in quantitative peptide data) VDJsolver Immunological features and many other tools online
SolyPep Random peptide library generation, accounting or not for solubility, and preparing for docking       online
PepMapper A collaborative web tool for mapping epitopes from affinity-selected peptides       online
CSA Comprehensive comparison of pairwise protein structure alignments       online
Super A web server to rapidly screen superposable oligopeptide fragments from the protein data bank       online
MCPep Monte Carlo simulations of peptide-membrane interactions with the MCPep web server       online
Paratome An online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure       online
iAMP-2L A two-level multi-label classifier for identifying antimicrobial peptides and their functional types       online
MESSA MEta-Server for protein Sequence Analysis       online
Scaffold A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins       online
Mutator Improving the selectivity of antimicrobial peptides from anuran skin       online
GibbsCluster  Simultaneous alignment & clustering of peptide data using a Gibbs sampling approach       online
SVMTriP  Predict antigenic epitopes (Realistic prediction of protein surface regions that are preferentially recognized by antibodies (antigenic epitopes) can help the design of vaccine components and immuno-diagnostic reagents)       online
PepSite  Prediction of peptide-binding sites        online docking
PeptiMap Detection of peptide-binding sites on protein surfaces        standalone from the authors, server on the way
CellPPD Designing of Cell Penetrating Peptides        online
ElliPro Antibody Epitope Prediction        online
BCPREDS B-cell epitope prediction server online
Pepitope  Epitope mapping using affinity-selected peptides        online
LINK PepMapper seems to outperform MimoPro or Pep-3D-Search. PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides        online
BriX Database of protein fragments. Loop BriX contains loop fragments from 14.525 proteins.         database
RosettaAntibody Antibody variable region homology modeling server        online
Abysis The antibody database integrates sequence data from Kabat, IMGT and the PDB with structural data from the PDB        Antibody database
DOMINO  An open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains  database
pepMMsMIMIC pepMMsMIMIC: using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-peptide recognition of this natural peptide using both pharmacophore and shape similarity techniques (Swimming into peptidomimetic chemical, NAR 2011) peptides to chemical via screening online
POW Structure-based predictor of PDZ domain-peptide interactions online
LINK BHAGEERATH-H: A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction         online
LINK BHAGEERATH : An Energy Based Protein Structure Prediction Server         online
LINK Standardizing and simplifying analysis of Peptide library data standalone
LINK Standardizing and simplifying analysis of Peptide library data online
Innovagen Innovagen's peptide calculator makes calculations and estimations on some physiochemical properties online peptide physchem
PEP-FOLD Prediction of the 3D structure of peptides, linear and cyclic         online
PeptideLocator PeptideLocator: prediction of bioactive peptides in protein sequences online, need at present a UniProt IDs as input for the computation
EpiDOCK EpiDOCK: a molecular docking-based tool for MHC class II binding prediction online
Haddock Haddock to predict peptide-protein interaction (peptides recognize hot spot (see Stein and Aloy, PLoS One 3: e2524, 2008). Peptide binding sites can be predicted by tools such as PepSite (see also Ben-Shimon, Eisenstein,  2010, J Mol Biol 402). Haddock is compared to DynaDock and the FlexPepDock webserver (see Trellet et al., PLoS One. 2013;8(3):e58769) standalone and online
PepBank  A database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored        database
PEPsolubility Predict peptide solubility        online
LINK OPM database and PPM web server: resources for positioning of proteins in membranes        online, can also be interesting to design peptides
LINK FlexPepDock Rosetta FlexPepDock: The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor. See also FlexPepDock ab initio        online
LINK PEPstr : predict the tertiary structure of small peptides        online
LINK ProBuilder, build a sequence in 3D        online
LINK AVPpred antiviral peptides, also allow to get several properties of a sequence, polar, possible 3D structure, physchem etc        online
LINK Super: screen superposable oligopeptide fragments from the protein data bank        online
LINK PepMake generates a PDB coordinate file for polypeptide backbones using only the sequence and backbone dihedral angles as input        online
LINK MODPROPEP: knowledge-based modeling of protein-peptide complexes standalone
LINK SLiMDisc (Short Linear Motif Discovery): find shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner online
LINK the Bioware webserver contains several tools for short linear motif discovery and peptide characterisation. CycloPsWeb with logP, etc, PeptideRanker, PeptideLocator online
LINK PepX contains many unique protein-peptide interface from the PDB. February 2013, it contains 505 unique protein-peptide interface clusters from 1431 PDBs database
PepCrawler PepCrawler high-resolution refinement and binding affinity estimation of peptide inhibitors online
PepServe A web server for peptide analysis, clustering and visualization online
PeptideMine  A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes online, PPI
IBIS  Inferred Biomolecular Interaction Server reports, predicts and integrates multiple types of conserved interactions for proteins. IBIS provided annotations for 5 different types of binding partners: proteins, PPI, small molecules, nucleic acids and peptides and ion online, also binding site
ParDOCK Protein-Ligand Complexes, might dock peptides (it is an all-atom energy based Monte Carlo,rigid protein ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the ligand in receptor target site) online
PROFEAT  Protein Feature Server for computing physicochemical properties of proteins and peptides online
NOXclass Prediction of protein-protein interaction types (biological obligate, biological non-obligate and crystal packing) implemented using a support vector machine (SVM) algorithm online
DILIMOT A server for finding short (3-8 amino acids), over-represented peptide patterns, or Linear motifs, in a set of proteins online
SLiMFinder A web server to find novel, significantly over-represented, short protein motifs online
ELM A computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional site prediction using as input aa sequence. Can be used to search PPI online