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Tertiary protein structure prediction software tools | Biomolecular structure

RCSB PDB
Dataset

RCSB PDB The Research Collaboratory for Structural Bioinformatics Protein Data Bank

Helps students and researchers to understand all aspects of biomedicine and…

Helps students and researchers to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. RCSB PDB is a database that provides a resource powered by the…

ProteinLounge
Web

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,…

RaptorX
Desktop
Web

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…

IntFOLD
Web

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…

OPM
Dataset

OPM Orientations of Proteins in Membranes

Provides spatial positions of membrane-bound peptides and proteins of known 3D…

Provides spatial positions of membrane-bound peptides and proteins of known 3D structure in the lipid bilayer. OPM is a curated web resource which contains more than 1200 transmembrane and peripheral…

SWISS-MODEL
Web

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.

ENDscript
Web

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.

CPHmodels
Web

CPHmodels

Predicts protein 3D structure by using single template homology model.…

Predicts protein 3D structure by using single template homology model. CPHmodels was created to make a front-end that was easy to understand for users without any prior knowledge of homology…

FRAGFOLD
Desktop

FRAGFOLD

Allows prediction of protein structure. FRAGFOLD can generate compact…

Allows prediction of protein structure. FRAGFOLD can generate compact structures with significant similarity to the experimentally determined structures even for proteins with entirely novel folds.…

Robetta
Web

Robetta

Provides automated structure prediction and analysis tools to infer protein…

Provides automated structure prediction and analysis tools to infer protein structural information from genomic data. Robetta uses a fully automated implementation of the Rosetta software package for…

RaptorX-Propert…
Web

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…

Proteopedia
Dataset

Proteopedia

Stores 3D structures of proteins and other molecules, with descriptive text and…

Stores 3D structures of proteins and other molecules, with descriptive text and hyperlinks that change the adjacently displayed structures to coincide with points made in the text. Proteopedia is a…

MMDB
Dataset

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…

I-TASSER
Web
Desktop

I-TASSER Iterative Threading ASSEmbly Refinement

Allows automated protein structure prediction and structure-based function…

Allows automated protein structure prediction and structure-based function annotation. I-TASSER constructs, starting from the amino acid sequence, 3D structural models by reassembling fragments…

SABBAC
Web
TASSER-Lite
Web

TASSER-Lite Threading/ ASSembly/Refinement Lite

Provides a comparative modeling tool. TASSER-Lite can be apply to the…

Provides a comparative modeling tool. TASSER-Lite can be apply to the large-scale comparative modeling and is mainly developed for homologous protein sequences. The search can be run from the website…

RW
Desktop

RW

Provides distance-dependent atomic potential for protein structure modeling and…

Provides distance-dependent atomic potential for protein structure modeling and structure decoy recognition. RW was derived from 1,383 high-resolution protein data bank (PDB) structures using an…

CNS
Desktop

CNS Crystallography & NMR System

Provides a flexible multi-level hierachical approach for the most commonly used…

Provides a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. CNS allows heavy atom searching, experimental phasing (including…

ANGULATOR
Web

ANGULATOR Angular Trends Of Repeat Proteins

Determines solenoid shaped repeat protein structures geometry. Angulator solves…

Determines solenoid shaped repeat protein structures geometry. Angulator solves curvature, twist, and lateral bending angles calculation. Each repeat is calculated according to the preceding repeat…

BetaSCPWeb
Web

BetaSCPWeb

Allows users to study amino acid sequence. BetaSCPWeb permits users to choose…

Allows users to study amino acid sequence. BetaSCPWeb permits users to choose rotamers from three different rotamer libraries: the most recent backbone-dependent one in addition to the earlier…

ModWeb
Web

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…

CATH
Dataset

CATH

Comprises over 300 000 domain structures and over 53 million protein domains…

Comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies. Cath-Gene3D contains over 300 000 structural domains. It groups protein…

TOPSAN
Dataset

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.

BioJava-ModFind…
Desktop

BioJava-ModFinder

Identifies protein modifications observed in 3-D structures archived in the…

Identifies protein modifications observed in 3-D structures archived in the Protein Data Bank (PDB). BioJava-ModFinder collects information on more than 400 types of protein modifications curated…

Edlib
Desktop

Edlib

Calculates exact pairwise sequence alignment using edit distance. Edlib…

Calculates exact pairwise sequence alignment using edit distance. Edlib supports the global alignment method and the semi-global alignment method where gaps at the end of the query sequence are not…

SPIDER
Web
Desktop
uQlust
Desktop

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…

MODICT
Desktop

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.…

JPred
Web

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…

OPUS-DOSP
Desktop

OPUS-DOSP

Provides a protein modeling and structure prediction method. OPUS-DOSP is a…

Provides a protein modeling and structure prediction method. OPUS-DOSP is a distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing. It also includes an…

(PS)2
Web

(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…

FANTEN
Web

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…

Frag'r'Us
Web

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.

PredictProtein
Web

PredictProtein

Provides a suite of methods important for the prediction of protein structural…

Provides a suite of methods important for the prediction of protein structural and functional features. predictProtein is a web server that incorporates over 30 tools. This software searches…

Cancer3D
Dataset

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…

WDSPdb
Dataset

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…

Genome3D
Dataset

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,…

PDBeMotif
Web

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.

TA-fold
Web

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…

CMsearch
Desktop

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…

UniCon3D
Desktop

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…

FALCON@home
Web

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…

SCEC
Web
3DBIONOTES
Web

3DBIONOTES

Allows users to automatically annotate structural models. 3DBIONOTES authorizes…

Allows users to automatically annotate structural models. 3DBIONOTES authorizes users to: (i) expose the macromolecular structure submitted or queried by users; (ii) show the biomedical and…

VisGrid
Desktop

VisGrid

Intends to identify protrusions, flat regions, hollows, together with pocket…

Intends to identify protrusions, flat regions, hollows, together with pocket regions in a protein surface. VisGrid aims to classify geometric features of protein surfaces using an intuitive concept…

LRRfinder
Web

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.

SIDEpro
Web

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.

ResQ
Web

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…

OPUS-PSP
Desktop

OPUS-PSP

Allows users to surmount the aforementioned drawbacks and bridge the gap…

Allows users to surmount the aforementioned drawbacks and bridge the gap between all-atom and residue-based potentials. OPUS-PSP captures the essential details of side-chain flexibility and packing…

Balloon
Desktop

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…

sDFIRE
Algorithm

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 the…

Protinfo
Web

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…

CABS-fold
Web

CABS-fold

Provides server for the ab initio and consensus-based prediction of protein…

Provides server for the ab initio and consensus-based prediction of protein structure. CABS-fold is a web application for protein structure, including de novo, modeling and comparative modeling using…

wwPDB
Dataset

wwPDB Worldwide PDB

Manages the deposition, processing and distribution of the Protein Data Bank…

Manages the deposition, processing and distribution of the Protein Data Bank (PDB) archive. wwPDB is a repository for the coordinates and related information for more than 38 000 structures,…

GOAP
Desktop

GOAP Generalized Orientation-dependent All-atom Potential

Implements a generalized orientation-dependent, all-atom statistical potential…

Implements a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. GOAP depends on the relative orientation of the planes associated with each heavy atom…

ROSIE
Web

ROSIE Rosetta Online Server That Includes Everyone

Identifies lipid accessible residues from a protein structure. ROSIE employs a…

Identifies lipid accessible residues from a protein structure. ROSIE employs a 2D concave hull algorithm on a point cloud onto the plane of the membrane. It can be applied to both α-helical and…

MPI…
Web

MPI Bioinformatics Toolkit

Provides access to a variety of public and in-house bioinformatics tools. The…

Provides access to a variety of public and in-house bioinformatics tools. The MPI Bioinformatics Toolkit integrates a selected set of most useful methods for the analysis of protein sequences and…

SAINT2
Desktop

SAINT2

Predicts fragment-assembly structure independently. SAINT2 can perform…

Predicts fragment-assembly structure independently. SAINT2 can perform predictions either sequentially, starting from either terminus, or non-sequentially, similar to traditional structure prediction…

GRAD
Desktop

GRAD GRadient Adaptive Decomposition

Provides an accurate definition of the energy barriers and related borders.…

Provides an accurate definition of the energy barriers and related borders. GRAD is a program using a noise-filtering procedure to smooth the energy landscape, reducing the roughness due to errors.…

M3
Desktop

M3 Model Molecular Machines

Allows users to determine quasi-atomic-resolution structures of molecular…

Allows users to determine quasi-atomic-resolution structures of molecular machines. M3 employs complementary and orthogonal experimental information such as interatomic distances and molecular…

E3FP
Desktop

E3FP Extended 3-Dimensional FingerPrint

Encodes 3D information without the need for molecular alignment, scales…

Encodes 3D information without the need for molecular alignment, scales linearly with 2D fingerprint pairwise comparisons in computation time. E3FP is an open-source inspired by Extended Connectivity…

PanDDA
Desktop

PanDDA Pan-Dataset Density Analysis

Analyses the data resulting from crystallographic fragment screening. PanDDA is…

Analyses the data resulting from crystallographic fragment screening. PanDDA is a package that comprises the characterization of a set of related crystallographic data sets of the same crystal form,…

PB-kPRED
Web

PB-kPRED

Serves to predicting Protein Blocks (PB) sequence from amino acid sequence.…

Serves to predicting Protein Blocks (PB) sequence from amino acid sequence. PB-kPRED takes no other inputs than the amino acid sequence of a query and interrogates a database of pentapeptides…

GAPlus
Desktop

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…

RCSB PDB Mobile
Mobile
FiltRest3D
Web

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…

Pro-Origami
Web

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…

GDFuzz3D
Desktop
Web

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…

SpeeDB
Web

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.…

AMASS
Dataset

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.

MODAS
Web

MODAS MODular Approach to Structural class prediction

Exploits sequence and sequence-derived information to generate input for the…

Exploits sequence and sequence-derived information to generate input for the classifier. MODAS a prediction method that combines both multiple sequence alignment (MSA) profiles and predicted…

QuaBingo
Web

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,…

Seder
Desktop

Seder

Provides a global protein structure method. Seder is a knowledge-based function…

Provides a global protein structure method. Seder is a knowledge-based function that scores protein decoys based on their similarity to native structure. It provides a set of features constructed to…

T-RMSD
Web
Desktop

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…

Phyre
Web

Phyre

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…

VLDP
Web

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…

PELE
Web

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…

DomIns
Dataset

DomIns

Provides information on domain insertions in known protein structures. DomIns…

Provides information on domain insertions in known protein structures. DomIns is a web resource using the Structural Classification of Proteins (SCOP) protein domain definitions to identify…

Flib
Desktop

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…

IRECS
Desktop

IRECS iterative REduction of Conformational Space

Predicts the conformation of protein side chains. IRECS ranks all side-chain…

Predicts the conformation of protein side chains. IRECS ranks all side-chain rotamers of a protein according to the probability with which each side chain adopts the respective rotamer conformation.…

SBION
Desktop

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…

mp lipid acc
Web

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…

CCP4
Desktop

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…

MTMG
Desktop

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…

MULTICOM
Web
Desktop

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…

EVA
Dataset

EVA

Aims to evaluate the accuracy of automated protein structure prediction…

Aims to evaluate the accuracy of automated protein structure prediction methods. EVA is updated automatically each week, to cope with the large number of existing prediction servers and the constant…

SSpro/ACCpro
Desktop
Web

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.

SKINK
Web

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.

ARP/wARP
Web
Desktop

ARP/wARP

Builds a protein model into an electron density map. ARP/wARP facilitates model…

Builds a protein model into an electron density map. ARP/wARP facilitates model building by initially interpreting a density map with free atoms of unknown chemical identity; all structural…

PDB-Explorer
Web

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…

SCWRL
Desktop

SCWRL

Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer…

Determinates side-chain conformations. SCWRL uses a backbone-dependent rotamer library, a simple energy function based on the library rotamer frequencies and a purely repulsive steric energy term,…

OPUS-Rota
Desktop

OPUS-Rota

Models side-chain conformation. OPUS-Rota uses simulated annealing by heat bath…

Models side-chain conformation. OPUS-Rota uses simulated annealing by heat bath Monte Carlo as a sampling method, which is able to rapidly identify near-native conformations when combined with…

ProBar
Desktop

ProBar Protein Barcode

Represents protein structure in the form of a barcode and locate them in a…

Represents 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 of this type of…

SVM-PB-Pred
Web

SVM-PB-Pred

Predicts the Protein Block (PB) for any given amino acid sequence. The input…

Predicts the Protein Block (PB) for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or…

BEGDB
Dataset

BEGDB Benchmark Energy and Geometry DataBase

Collects results of highly accurate QM (quantum mechanics) calculations of…

Collects results of highly accurate QM (quantum mechanics) calculations of molecular structures, energies and properties. BEGDB hosts data which can serve as benchmarks for testing and…

CAMEO
Dataset

CAMEO Continuous Automated Model EvaluatiOn

Evaluates the accuracy and reliability of protein structures, ligand binding…

Evaluates the accuracy and reliability of protein structures, ligand binding sites and quality models predictions. CAMEO is a community project that works in a fully automated manner. This project…

Twilight
Desktop

Twilight

Aims to simplify electron-density-map-based visualization, analysis,…

Aims to simplify electron-density-map-based visualization, analysis, validation, annotation and correction of ligand molecules found in protein structures determined by X-ray crystallography.…

FUSION
Web

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…

3D-SURFER
Web

3D-SURFER

Allows high-throughput protein surface comparison, analysis, and visualization.…

Allows high-throughput protein surface comparison, analysis, and visualization. 3D-SURFER is a web-based platform that compares the protein surface of a single chain, a single domain, or a single…

3D Protein…
Web

3D Protein Retrieval

Compares the protein structure from multiple viewpoints. 3D Protein Retrieval…

Compares the protein structure from multiple viewpoints. 3D Protein Retrieval is based on LightField descriptors to match 3D protein structures in visual-based similarity. The concept of the…

Pcons5
Desktop

Pcons5

Integrates information from three different sources: the consensus analysis,…

Integrates information from three different sources: the consensus analysis, structural evaluation and the score from the fold recognition servers. Pcons5 is an improved version of the consensus…

Voroprot
Desktop

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…

CMM
Desktop

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…

pDomTHREADER
Web

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…

Bhageerath-H
Web

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…

ROTAS
Desktop

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,…

PHAISTOS
Desktop

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…

COSMOS
Web

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…

chunk-TASSER
Web

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.

eThread
Desktop
Web

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.

MetaTASSER
Web
Desktop

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…

MUFOLD
Web

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…

QUARK
Web

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…

TASSER-VMT
Web

TASSER-VMT

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

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

BASILISK
Desktop
GalaxyTBM
Web

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…

BioSuper
Web

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…

KINARI-Curation
Web

KINARI-Curation

Allows users to clean PDB files. KINARI-Curation is a suite of tools that…

Allows users to clean PDB files. KINARI-Curation is a suite of tools that lists, for a given PDB file, the models, chains, ligands, water molecules and more, included into this file. It also permits…

PDB Editor
Desktop

PDB Editor Protein Data Bank File Editor

Edits and extracts raw information from protein data bank (PDB) files. PDB…

Edits and extracts raw information from protein data bank (PDB) files. PDB Editor allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is…

pcSM
Web

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,…

PSAweb
Web

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…

CHpredict
Desktop
Web

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…

Ar_NHPred
Desktop
Web

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…

OPENSEQ
Desktop
Web

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.…

3DSwap
Dataset

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.

iPfam
Dataset

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.

EdaRose
Desktop

EdaRose

Allows protein structure prediction. EdaRose is a fragment-based protein…

Allows protein structure prediction. EdaRose is a fragment-based protein structure prediction method that combines the simulated annealing sampler from Rosetta AbRelax and the estimation of…

Voronota
Desktop

Voronota

Implements a simple and robust algorithm for computing the vertices of the…

Implements a simple and robust algorithm for computing the vertices of the Voronoi diagram of balls. The Voronota algorithm is particularly well-suited for processing 3D structures of biological…

LOCUSTRA
Web

LOCUSTRA

Predicts the local structure of a protein chain from its sequence. LOCUSTRA is…

Predicts the local structure of a protein chain from its sequence. LOCUSTRA is a scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). This…