A Guide to Structure Prediction
NIH Research Resource Center for the Development of Multiscale Modeling Tools for Structural Biology
Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.
The current version of Mol2Mol
Remediator converts PDB files between PDBv2.3 and PDBv3.0 formats.
Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to support of the CASP meetings our goal is to promote an evaluation of prediction methods on a continuing basis (note: not a resource).
The BioInfoBank Meta Server offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the prediction servers are assessed using the powerful 3D-jury consensus approach.
This meta-server, named @TOME V2, allows one to submit an amino acid sequence to embedded softwares dedicated to homologous sequences search, structural predictions and fold recognition.
Protein Structure Prediction Meta Server.
This is a gateway to various methods for protein structure prediction.
Protein & Drug Design & Modelling Platforms
RosettaDesign is a high resolution structure prediction and design software which identifies low energy sequences for specified protein backbones, and has been used previously to stabilize proteins and create new protein structures.
MODELLER isa widely used platform for homology or comparative modeling of protein three-dimensional structure.
WHAT IF is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
The program TRITON is a graphical tool for computational aided protein engineering. It implements methodology of computational site-directed mutagenesis to design new protein mutants with required properties. It uses the external program MODELLER to model structures of new protein mutants based on the wild-type structure by homology modelling method. Subsequently, properties of these protein mutants are modelled.
BRAGI: A well-established package for Protein Visualization and Modeling
A Multi-platform 3D Stereo Molecular Dynamics Trajectory Visualization Package
AstexViewer is a Java molecular graphics program that assists in structure based drug design.
Yammp Under Python (YUP), also known as Yammp 2, is a molecular modeling program. Although a general purpose tool, development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp.
3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations
Jackal is a collection of programs designed for the modeling and analysis of protein structures.
AMMP is a molecular mechanics and dynamics program. AMMP is a fully featured molecular modeling program.
INTERCHEM is a general purpose molecular modelling program written by Robin Breckenridge and Peter Bladon of the University of Strathclyde.
Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work. It is equally suited for protein and small molecule construction and visualization.
CPHmodels 2.0 is a homology modeling server.
3D-JIGSAW builds three-dimensional models for proteins based on homologues of known structure
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane ?-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS2 is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2=94%), membrane spanning helices (Q2=87%) and secondary structure (Q3 score of 81.3% )
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via e-mail.
ESyPred3D is a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks.
Full chain protein structure prediction server.
Fold & Function Assignment System
Comparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments.
A Server for Protein Structure Modeling.
(PS)2 is an automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment.
Online Protein Structural Prediction Pipeline
AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
The present version of 'Bhageerath' accepts amino acid sequence and secondary structure information to predict 10 candidate structures for the native. It is anticipated that at least one native like structure (RMSD < 6
A Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information.
Protein Homology/analogY Recognition Engine
DescFold(Descriptor-based Fold Recognition System) is a web server for protein fold recognition,which can predict a protein's fold type from its amino acid sequence. The server combines six effictive descriptors : a profile-sequence-alignment-based descriptor using Psi-blast e-values and bit scores, a sequence-profile-alignment-based descriptor using Rps-blast e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), a descriptor based on the occurrence of PROSITE functional motifs, a descriptor based on profile-profile-alignment(PPA) and a descriptor based on Profile-structural-profile-alignment (PSPA) .
Homology detection & structure prediction by HMM-HMM comparison.
The nFOLD3 protein fold recognition server allows you to generate 3D models of a protein from its amino acid sequence. This new version of nFOLD uses the ModFOLD model quality assessment program to rank models built from several profile-profile alignment methods, which are run in-house - SP3, SPARKS, and HHsearch.
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure.
HMM-based Protein Structure Prediction.
LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure. The signals we are using include straightforward sequence alignment, sequence profile, threading, secondary structure and exposed surface area prediction.
prediction of fold using protein interactions.
FORTE: a profile-profile comparison tool for protein fold recognition.
Fold-recognition services based on Sequence-Derived Properties, combining old and new methods.
ModLoop is a web server for automated modeling of loops in protein structures.
A template-based lopp prediction server.
The Loop Homology Modeling Server is a tool to predict protein loop backbone structures from their sequences and their flank backbone structures.
SuperLooper provides an online interface for the automatic, quick and interactive search and placement of loops in proteins.
RAPPER is an ab initio conformational search algorithm for restraint-based protein modelling.