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Loop structure prediction software tools | Protein structure data analysis

Protein loops are often responsible for functional specificity of a given protein by contributing to recognition of interaction partners, enzymatic reactions with substrates or conformational changes relevant to function. The special properties of…
ABGEN
Desktop

ABGEN AntiBody structure GENeration

Obtains structural models of antibody fragments. ABGEN utilizes a homology…

Obtains structural models of antibody fragments. ABGEN utilizes a homology based scaffolding technique, and includes the use of invariant and strictly conserved residue replacements and key…

SuperLooper
Web

SuperLooper

Provides a scoring function for knowledge based loop predictions. SuperLooper…

Provides a scoring function for knowledge based loop predictions. SuperLooper provides information on sequence identities or proline and glycine exchanges between the template and the target, as well…

RCD+
Web

RCD+ Random Coordinate Descent +

A quick online service for ab initio loop modeling combining a coarse-grained…

A quick online service for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. RCD+ is an upgrade of the original Random Coordinate Descent loop…

Sphinx
Web

Sphinx

Combines knowledge-based and ab initio approaches. Sphinx is a protein loop…

Combines knowledge-based and ab initio approaches. Sphinx is a protein loop modelling algorithm that generate high-accuracy predictions and decoy sets enriched with near-native loop conformations.…

BCSearch
Web

BCSearch

Facilitates large-scale mining of protein structures. BCSearch undergoes…

Facilitates large-scale mining of protein structures. BCSearch undergoes several tens of thousands of comparisons per second. It performs a search for similar fragment search within large collections…

ArchDB
Dataset

ArchDB

A structural classification of loops extracted from known protein structures.…

A structural classification of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four…

LoopIng
Web

LoopIng

A method based on the Random Forest automated learning technique, which, given…

A method based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently…

NORSnet
Desktop

NORSnet

Identifies unstructured loops from sequence. NORSnet was accurate to flag…

Identifies unstructured loops from sequence. NORSnet was accurate to flag unstructured regions in proteins that were previously not annotated. It predicts information rather than on experimental data…

ArchPRED
Web

ArchPRED

Implements a fragment-search based method for predicting loop conformations.…

Implements a fragment-search based method for predicting loop conformations. The inputs to the server are the atomic coordinates of the query protein and the position of the loop. The algorithm…

FALC-Loop
Desktop
Web

FALC-Loop

Provides an online interface for protein loop modeling by employing an ab…

Provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct…

DISGRO
Desktop

DISGRO Distance-guided Sequential chain-Growth Monte Carlo

A protein loop sampling and structure prediction tool based on distance-guided…

A protein loop sampling and structure prediction tool based on distance-guided sequential chain-growth Monte Carlo method. DISGRO can efficiently generate high quality near-native loop conformations…

ModLoop
Web

ModLoop

A web server for automated modeling of loops in protein structures. ModLoop…

A web server for automated modeling of loops in protein structures. ModLoop relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints,…

LEAP
Desktop

LEAP

A coarse-grained, optimized scoring function for initial sampling and ranking…

A coarse-grained, optimized scoring function for initial sampling and ranking of loop decoys. The resulting decoys are then further optimized in backbone and side-chain conformations and ranked by…

SmrtMolAntibody
Web

SmrtMolAntibody

Takes an input antibody sequence and returns an energy optimized accurate…

Takes an input antibody sequence and returns an energy optimized accurate structure in minutes. SmrtMolAntibody is part of a suite of modeling tools provided by Macromoltek. It creates a structure of…

OSCAR
Desktop

OSCAR Optimized Side-Chain Atomic eneRgy

Permits to models protein side-chain. OSCAR proposes several functions as (1)…

Permits to models protein side-chain. OSCAR proposes several functions as (1) OSCAR-o for orientation-dependent energy functions and (2) OSCAR-d for distance-dependent energy functions. This tool was…

FREAD
Web

FREAD

A database search loop modelling algorithm. Its primary use is to fill in the…

A database search loop modelling algorithm. Its primary use is to fill in the gaps in incomplete 3D models of protein structures. The input is a 3D model of a protein structure as well as the…

BioLuminate
Desktop

BioLuminate

Provides a comprehensive modeling solution for biologics. BioLuminate is a user…

Provides a comprehensive modeling solution for biologics. BioLuminate is a user interface and the kynchpin product of the Biologics Suite that is designed from the ground up, with significant user…

LoopTK
Desktop

LoopTK

Analyzing the motion of flexible protein loops is becoming increasingly…

Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit…

LIP
Dataset

LIP Loops In Proteins

Includes all protein segments of a length up to 15 residues contained in the…

Includes all protein segments of a length up to 15 residues contained in the Protein Data Bank (PDB). Searching the database for loop candidates takes less than 1 s on a desktop PC, and ranking them…

CODA
Web

CODA

An algorithm for predicting the variable regions in proteins, combines FREAD a…

An algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. CODA shows a general improvement in loop…

WAM
Desktop

WAM Web Antibody Modelling

Offers an improved algorithm for complementarity determining region (CDR)-H3…

Offers an improved algorithm for complementarity determining region (CDR)-H3 modelling. WAM has been launched as an online modelling service. It constructs 3D models of antibody variable region…

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