Desktop app
uQlust uQlust

uQlust

Ranks and clusters macromolecular structures, including proteins and RNAs.…

Ranks and clusters macromolecular structures, including proteins and RNAs. uQlust combines versatile structural profiles of both proteins and nucleic acids with linear time algorithm for comparison…

Web app
Finding ANisotropy… Finding ANisotropy TENsors

FANTEN Finding ANisotropy TENsors

Determines the anisotropy tensors related to PCSs and RDCs. FANTEN allows the…

Determines the anisotropy tensors related to PCSs and RDCs. FANTEN allows the users to determine the anisotropy tensors through a joint analysis of these restraints. It can be used to predict PCS and…

Web app
FiltRest3D FiltRest3D

FiltRest3D

A server for scoring and ranking of models according to their agreement with…

A server for scoring and ranking of models according to their agreement with user-defined restraints. FILTREST3D is a standalone open source Python program. The scoring function is a simple sum of…

Desktop app
Balloon Balloon

Balloon

A multi-objective genetic algorithm for the generation of conformer ensembles.…

A multi-objective genetic algorithm for the generation of conformer ensembles. Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and conformer ensembles. The…

Web app
ModWeb ModWeb

ModWeb

A comparative modeling web-server for protein structure modelling closely…

A comparative modeling web-server for protein structure modelling closely connected to ModBase. ModWeb accepts one or many sequences in the FASTA format and calculates their models using ModPipe…

Desktop app
Collaborative… Collaborative Computational Project 4

CCP4 Collaborative Computational Project 4

A collection of programs, associated data and software libraries which can be…

A collection of programs, associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. CCP4 is designed to be flexible, allowing users…

Web app
Pro-Origami Pro-Origami

Pro-Origami

Generates protein structure cartoons. Pro-Origami web server allows diagrams to…

Generates protein structure cartoons. Pro-Origami web server allows diagrams to be generated from any Protein Data Bank (PDB) file. The resulting diagram may be either downloaded or viewed as an SVG…

Web app
Rosetta Online Server… Rosetta Online Server That Includes Everyone

ROSIE Rosetta Online Server That Includes Everyone

A web front-end to the Rosetta software suite. ROSIE is a molecular modeling…

A web front-end to the Rosetta software suite. ROSIE is a molecular modeling software package that provides experimentally tested and rapidly evolving tools for the 3D structure prediction and…

Desktop app
MODICT MODICT

MODICT

A mutation prediction tool which is based on per residue root mean square…

A mutation prediction tool which is based on per residue root mean square deviation values of superimposed 3D protein models. MODICT predicts the effect of mutations on the structure of the protein.…

Desktop app
Twilight Twilight

Twilight

A software script that aims to simplify electron-density-map-based…

A software script that aims to simplify electron-density-map-based visualization, analysis, validation, annotation and correction of ligand molecules found in protein structures determined by X-ray…

Web app
RaptorX-Property RaptorX-Property

RaptorX-Property

A web server predicting structure property of a protein sequence without using…

A web server predicting structure property of a protein sequence without using any templates. RaptorX-Property outperforms other servers, especially for proteins without close homologs in PDB or with…

Desktop app
Voroprot Voroprot

Voroprot

An interactive cross-platform software tool that provides a unique set of…

An interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the…

Desktop app
SBION SBION

SBION

Provides binary items in excel format along with details on intra and…

Provides binary items in excel format along with details on intra and inter-dipole interactions and orientations. SBION provides intricate details on salt-bridges and finds application in structural…

Web app
TA-fold TA-fold

TA-fold

Classifies the protein fold by combing the results from two algorithms, HH-fold…

Classifies the protein fold by combing the results from two algorithms, HH-fold and support vector machines (SVM)-fold. TA-fold is an ensemble approach proposed to combine the results of these…

Web app
mp lipid acc mp lipid acc

mp lipid acc

Indentifies lipid accessible residues from the protein structure, implemented…

Indentifies lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. mp_lipid_acc method uses protein structures transformed in…

Desktop app
PHAISTOS PHAISTOS

PHAISTOS

A software framework for Markov chain Monte Carlo (MCMC) sampling for…

A software framework for Markov chain Monte Carlo (MCMC) sampling for simulation, prediction, and inference of protein structure. PHAISTOS contains implementations of recently developed tools that…

Web app
COordinates of Small… COordinates of Small MOleculeS

COSMOS COordinates of Small MOleculeS

A 3D structure predictor. COSMOS is a high-throughput method to predict the 3D…

A 3D structure predictor. COSMOS is a high-throughput method to predict the 3D structure of small molecules from their 1D/2D representations. This data-driven algorithm predicts 3D molecule…

Web app
ResQ ResQ

ResQ

Estimates residue-specific quality of protein structure prediction and the…

Estimates residue-specific quality of protein structure prediction and the inherent B-fac for profile of all residues along the chain. ResQ takes into the consideration of the intermediate procedures…

Desktop app
CMsearch CMsearch

CMsearch

Explores simultaneously protein sequence space and protein structure space by…

Explores simultaneously protein sequence space and protein structure space by cross-modal learning. CMsearch has several advantages over existing methods: (i) instead of exploring a single space…

Web app
QuaBingo QuaBingo

QuaBingo

A prediction system for the classification of protein quaternary structure.…

A prediction system for the classification of protein quaternary structure. QuaBingo is designed by three layers of classifiers that can categorize quaternary structural attributes of monomer,…

Web app
Desktop app
Meta Threading… Meta Threading ASSEmbly Refinemen

MetaTASSER Meta Threading ASSEmbly Refinemen

A package and a WUI for a protein tertiary prediction method. MetaTASSER…

A package and a WUI for a protein tertiary prediction method. MetaTASSER employs the 3D-Jury approach to select threading templates from SPARKS, SP3 and PROSPECTOR_3. This method provides aligned…

Web app
Desktop app
Sequence-based… Sequence-based Prediction of Local and Nonlocal…
Desktop app
Protein Barcode Protein Barcode

ProBar Protein Barcode

A visualization tool to represent protein structure in the form of a barcode…

A visualization tool to represent protein structure in the form of a barcode and locate them in a protein-barcode database by making use of content-based image retrieval (CBIR) tools. The advantage…

Desktop app
UniCon3D UniCon3D

UniCon3D

A de novo protein structure prediction method that performs stepwise synthesis…

A de novo protein structure prediction method that performs stepwise synthesis and assembly of foldon units via conditional sampling from a novel united-residue probabilistic model, which captures…

Desktop app
Multi-Template Model… Multi-Template Model Generation

MTMG Multi-Template Model Generation

A stochastic point cloud sampling method to address the challenges in…

A stochastic point cloud sampling method to address the challenges in generating structural models from multiple templates. MTMG first superposes the backbones of template structures, and the Cα…

Web app
MUFOLD MUFOLD

MUFOLD

A comprehensive platform for efficient and consistently accurate protein…

A comprehensive platform for efficient and consistently accurate protein tertiary structure prediction. MUFOLD platform provides pdbLight, a web-based database which integrates protein sequence and…

Web app
pcSM pcSM

pcSM

A physico-chemical based scoring metric to detect native or native-like…

A physico-chemical based scoring metric to detect native or native-like structures from pool of decoys. pcSM comprises of various parameters viz. Euclidian distance metric, surface accessible areas,…

Web app
3DBIONOTES 3DBIONOTES

3DBIONOTES

A web application that integrates protein sequence and structure in a unique…

A web application that integrates protein sequence and structure in a unique environment, unifying the accession to three of the most relevant protein resources: EMDB, PDB and UniProt. The design of…

Web app
FUSION FUSION

FUSION

A fragment-free probabilistic graphical model for conformational sampling in…

A fragment-free probabilistic graphical model for conformational sampling in continuous space. FUSION captures local relationships between protein sequence and structural features and allows for…

Web app
Desktop app
MULTICOM MULTICOM

MULTICOM

Combines multiple sources of information and complementary methods at all five…

Combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model…

Web app
Desktop app
Tree-based on… Tree-based on Root-Mean-Square Deviation

T-RMSD Tree-based on Root-Mean-Square Deviation

A fine-grained structural clustering method available within the T-Coffee web…

A fine-grained structural clustering method available within the T-Coffee web server. Given a set of structurally related proteins or protein families, T-RMSD will generate a supported structural…

Web app
QUARK QUARK

QUARK

A computer algorithm for ab initio protein folding and protein structure…

A computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from…

Desktop app
GAPlus GAPlus

GAPlus

A software tool for Ab initio protein structure prediction. The whole…

A software tool for Ab initio protein structure prediction. The whole optimization process is controlled by an enhanced genetic algorithm framework with four enhanced features: i) an exhaustive…

Web app
CABS-fold CABS-fold

CABS-fold

Provides tools for protein structure prediction from sequence only (de novo…

Provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling…

Web app
Bhageerath-H Bhageerath-H

Bhageerath-H

An automated pipeline for protein tertiary structure prediction. The pipeline…

An automated pipeline for protein tertiary structure prediction. The pipeline comprise six different modules which are Bhageerath-H Strgen for decoy generation, K-mean clustering, pcSM for decoy…

Web app
PDB-Explorer PDB-Explorer

PDB-Explorer

A color-coded interactive map of PDB in 3DP-space. Each pixel of the map…

A color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer…

Web app
FALCON@home FALCON@home

FALCON@home

A protein structure prediction server focusing on remote homologue…

A protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous…

Web app
Voronoi Laguerre… Voronoi Laguerre Delaunay Protein

VLDP Voronoi Laguerre Delaunay Protein

A set of accurate tools, for analysing protein structures, based on the…

A set of accurate tools, for analysing protein structures, based on the reliable method of Voronoi-Laguerre tessellations. The Voronoi Laguerre Delaunay Protein web server (VLDPws) computes the…

Desktop app
Flib Flib

Flib

A method for structure fragment library generation and its application in…

A method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. On a validation set of 41 structurally diverse proteins, Flib libraries…

Desktop app
Web app
GDFuzz3D GDFuzz3D

GDFuzz3D

A multi-step protocol that predicts protein 3D structures from the predicted…

A multi-step protocol that predicts protein 3D structures from the predicted contact maps. The method is based on a novel distance function acting on a fuzzy residue proximity graph, which predicts a…

Desktop app
CMM CMM

CMM

A statistical machine learning approach known as contrastive divergence to…

A statistical machine learning approach known as contrastive divergence to efficiently calculate a Maximum Entropy distribution that models the evolutionarily related family of a protein and have…

Web app
SpeeDB SpeeDB

SpeeDB

A web-based tool for the identification of protein structures based on…

A web-based tool for the identification of protein structures based on structural properties. SpeeDB queries are executed on all structures in the PDB at once, quickly enough for interactive use.…

Web app
GalaxyTBM GalaxyTBM

GalaxyTBM

Protein structures can be reliably predicted by template-based modeling (TBM)…

Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. GalaxyTBM is a TBM method in which the more reliable…

Web app
(PS)2 (PS)2

(PS)2

An automatic protein structure prediction server. (PS)2 uses an effective…

An automatic protein structure prediction server. (PS)2 uses an effective consensus strategy both in template selection, which combines PSI-BLAST and IMPALA. The method uses a new substitution…

Desktop app
Web app
eThread eThread

eThread

A template-based protein structure prediction approach. Template structures are…

A template-based protein structure prediction approach. Template structures are selected from the PDB library using meta-threading that combines ten individual threading/fold recognition algorithms.

Web app
I-TASSER I-TASSER

I-TASSER

An online resource for automated protein structure prediction and…

An online resource for automated protein structure prediction and structure-based function annotation. In I-TASSER, structural templates are first recognized from the PDB using multiple threading…

Web app
JPred JPred

JPred

A protein secondary structure prediction server. JPred incorporates the Jnet…

A protein secondary structure prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure, JPred also makes…

Worldwide PDB Worldwide PDB

wwPDB Worldwide PDB

The international collaboration that manages the deposition, processing and…

The international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for…

Web app
PredictProtein PredictProtein

PredictProtein

A meta-service for sequence analysis that has been predicting structural and…

A meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments,…

Web app
ProteinLounge ProteinLounge

ProteinLounge

Develops many interactive web-based databases and software to help the…

Develops many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks,…

Web app
BioSuper BioSuper

BioSuper

Provides immediate interactive visualization of the graphical results in the…

Provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based…

Web app
PSAweb PSAweb

PSAweb

A web server, developed to analyze the amino acid sequence and multiple…

A web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an…

Desktop app
Web app
CHpredict CHpredict

CHpredict

Predicts donor and acceptor residues in C alpha-H...O and C alpha-H...pi…

Predicts donor and acceptor residues in C alpha-H...O and C alpha-H...pi interactions in proteins. The method is based on the recurrent neural network (Jordan network) trained on single amino acid…

Desktop app
Web app
Ar_NHPred Ar_NHPred

Ar_NHPred

Predicts the aromatic-backbone NH (Ar-NH) interaction in a given amino acid…

Predicts the aromatic-backbone NH (Ar-NH) interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups. The method is based on the neural…

Cancer3D Cancer3D

Cancer3D

Gives an open and user-friendly way to analyze cancer missense mutations in the…

Gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. Cancer3D also helps users analyze the distribution patterns…

Web app
pDomTHREADER pDomTHREADER

pDomTHREADER

An accurate and sensitive superfamily discrimination, combining information…

An accurate and sensitive superfamily discrimination, combining information from both sequence and structure to produce highly accurate domain alignments. The method employs the same underlying…

Web app
Phyre2 Phyre2

Phyre2

Predicts the 3D structure of a protein sequence based on HMM-HMM alignment…

Predicts the 3D structure of a protein sequence based on HMM-HMM alignment techniques. For a given sequence, it detects known homologues based on PSI-Blast, constructs a hidden Markov model (HMM) of…

WDSPdb WDSPdb

WDSPdb

A free resource to provide high quality information of WD40 protein structures…

A free resource to provide high quality information of WD40 protein structures and hotspot residues. To better serve the community, a user-friendly interactive web interface to browse, search and…

CATH CATH

CATH

Provides information on protein structures that are related by evolution.…

Provides information on protein structures that are related by evolution. Protein structures (from the PDB) are chopped into structural domains then grouped into evolutionary superfamilies.

Genome3D Genome3D

Genome3D

Provides consensus structural annotations and 3D models for sequences from…

Provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP,…

Desktop app
Rotamer-dependent… Rotamer-dependent Statistical Atomic Potential

ROTAS Rotamer-dependent Statistical Atomic Potential

It is derived from known protein structures in the Protein Data Bank for…

It is derived from known protein structures in the Protein Data Bank for protein structure modeling and quality assessment. The basic building blocks of protein structures are amino acid residues,…

Desktop app
Web app
short for open… short for open sequence

OPENSEQ short for open sequence

Coevolution analysis of protein coding genes using GREMLIN. Database of…

Coevolution analysis of protein coding genes using GREMLIN. Database of precomputed results for all Pfam, E. coli genes and complexes. Web-server and software is provided for additional analysis.…

Web app
chunk-TASSER chunk-TASSER

chunk-TASSER

A protein structure prediction method that combines threading templates from…

A protein structure prediction method that combines threading templates from SP3 and ab initio folded chunk structures.

Web app
TASSER-VMT TASSER-VMT

TASSER-VMT

Builds target-template alignments using SP3 alternative alignment and HHpred…

Builds target-template alignments using SP3 alternative alignment and HHpred methods.

Desktop app
Web app
SSpro/ACCpro SSpro/ACCpro

SSpro/ACCpro

Trained modular versions of the SSpro and ACCpro predictors of secondary…

Trained modular versions of the SSpro and ACCpro predictors of secondary structure and relative solvent accessibility together with their multi-class variants SSpro8 and ACCpro20.

DomIns DomIns

DomIns

Aims to document domain insertions in known protein structures.

Aims to document domain insertions in known protein structures.

3DSwap 3DSwap

3DSwap

A comprehensive collection of protein structures that are reported to be…

A comprehensive collection of protein structures that are reported to be involved in 3-Dimensional Domain Swapping.

Web app
SWISS-MODEL SWISS-MODEL

SWISS-MODEL

The purpose of this server is to make Protein Modelling accessible to all…

The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide.

Web app
Robetta Robetta

Robetta

Provides automated tools for protein structure prediction and analysis.

Provides automated tools for protein structure prediction and analysis.

Web app
ENDscript ENDscript

ENDscript

A friendly Web server, which extracts and renders a comprehensive analysis of…

A friendly Web server, which extracts and renders a comprehensive analysis of primary to quaternary protein structure information in an automated way.

Desktop app
Web app
RaptorX RaptorX

RaptorX

A protein structure prediction server excelling at predicting 3D structures for…

A protein structure prediction server excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its…

Web app
IntFOLD IntFOLD

IntFOLD

An independent web server that integrates our leading methods for structure and…

An independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data…

Web app
SIDEpro SIDEpro

SIDEpro

A machine learning based program for the fast and accurate prediction of…

A machine learning based program for the fast and accurate prediction of side-chain conformations.

Web app
LRRfinder LRRfinder

LRRfinder

A web-based tool for the identification of leucine-rich repeats (LRRs) in…

A web-based tool for the identification of leucine-rich repeats (LRRs) in protein sequences.

Web app
Frag'r'Us Frag'r'Us

Frag'r'Us

A web server designed to sample alternative protein backbone conformations in…

A web server designed to sample alternative protein backbone conformations in loop regions.

Web app
SKINK SKINK

SKINK

Classifies given alpha-helical sequences into kinked and canonical helices…

Classifies given alpha-helical sequences into kinked and canonical helices based on a specified support vector machine (SVM) model.

Web app
3D-SURFER 3D-SURFER

3D-SURFER

A web-based tool for real-time protein surface comparison and analysis.

A web-based tool for real-time protein surface comparison and analysis.

AMASS AMASS

AMASS

Maps 1D sequence annotation databases to 3D protein structures with an…

Maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface.

The Research… The Research Collaboratory for Structural…

RCSB PDB The Research Collaboratory for Structural Bioinformatics Protein Data Bank

A resource powered by the Protein Data Bank archive - information about the 3D…

A resource powered by the Protein Data Bank archive - information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of…

Proteopedia Proteopedia

Proteopedia

The free, collaborative 3D-encyclopedia of proteins & other molecules.

The free, collaborative 3D-encyclopedia of proteins & other molecules.

Web app
PDBeMotif PDBeMotif

PDBeMotif

An extremely fast and powerful search tool that facilitates exploration of the…

An extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search.

Molecular Modeling… Molecular Modeling Database

MMDB Molecular Modeling Database

Provides a complete set of detailed and pre-computed structural alignments…

Provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the…

iPfam iPfam

iPfam

Catalogues Pfam domain interactions based on known 3D structures that are found…

Catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level.

Orientations of… Orientations of Proteins in Membranes

OPM Orientations of Proteins in Membranes

A curated web resource that provides spatial positions of membrane-bound…

A curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural…

Web app
Protinfo Protinfo

Protinfo

Predicts the tertiary and secondary structure of a protein, given its amino…

Predicts the tertiary and secondary structure of a protein, given its amino acid sequence. Protinfo enables users to submit a protein sequence and to request a prediction of the three dimensional…

sDFIRE sDFIRE

sDFIRE

An algorithm for protein structure prediction. sDFIRE outperforms other…

An algorithm for protein structure prediction. sDFIRE outperforms other state-of-the-art energy functions in selecting near native structures and in the Pearson’s correlation coefficient between…

Web app
Protein Energy… Protein Energy Landscape Exploration

PELE Protein Energy Landscape Exploration

This technology based on protein structure prediction algorithms and a Monte…

This technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast…

The Open Protein… The Open Protein Structure Annotation Network

TOPSAN The Open Protein Structure Annotation Network

A web-based collaboration platform for exploring and annotating structures…

A web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts.

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