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Coiled-coil domain detection software tools | Protein structure data analysis

Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a…
COILS/PCOILS
Web

COILS/PCOILS

Compares a single sequence (COILS) or a sequence alignment (PCOILS) to a…

Compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence…

COILCHECK
Web

COILCHECK

Allows users to identify and compare weak and strong regions within coiled-coil…

Allows users to identify and compare weak and strong regions within coiled-coil structures. COILCHECK contains functions for hydrogen atom fixing and hydrogen bond energy calculation to accurately…

CCFold
Desktop
Web

CCFold

Predicts coiled-coil structures. CCFold is a generally applicable…

Predicts coiled-coil structures. CCFold is a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence. The software is based on picking multiple CC…

PrOCoil
Desktop
Web

PrOCoil

An SVM-based classification method for predicting whether a given coiled coil…

An SVM-based classification method for predicting whether a given coiled coil sequence is a trimer or dimer (assuming that it is one of both). PrOCoil also allows for a deep analysis of the sequence…

Waggawagga
Web

Waggawagga

A web-based tool for the comparative visualization of coiled-coil predictions…

A web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single alpha-helices (SAH domains). Overview schemes show the predicted coiled-coil regions…

CCBuilder
Web

CCBuilder

Tackles the problem for a defined but large class of protein structure, the…

Tackles the problem for a defined but large class of protein structure, the alpha-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and…

CC model
Desktop

CC model Coiled-coil specific model

A model of evolution that improves phylogeny inference and homology detection…

A model of evolution that improves phylogeny inference and homology detection of coiled-coils. CC model outperforms general models in phylogeny inference for coiled-coil rich proteins, giving trees…

CC+
Dataset

CC+

A detailed, searchable repository of coiled-coil assignment. Coiled coils were…

A detailed, searchable repository of coiled-coil assignment. Coiled coils were identified using the program SOCKET, which locates coiled coils based on knobs-into-holes packing of side chains between…

RFCoil
Desktop
Web

RFCoil

A predictor that could distinguish parallel dimeric and trimeric coiled coils.…

A predictor that could distinguish parallel dimeric and trimeric coiled coils. RFCoil uses the most efficient and non-redundant amino acid indices combined with the state-of-the-art machine learning…

Paircoil
Desktop
Web

Paircoil

Uses pairwise residue probabilities to detect coiled-coil motifs in protein…

Uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out…

SCORER
Desktop
Web

SCORER

An algorithm for distinguishing parallel dimeric and trimeric coiled-coil…

An algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. SCORER is particularly useful for researchers looking to characterize novel coiled-coil sequences. It may also be…

MARCOIL
Desktop
Web

MARCOIL

A hidden Markov model-based program that predicts existence and location of…

A hidden Markov model-based program that predicts existence and location of potential coiled-coil domains in protein sequences. A cross-validated study suggests that MARCOIL improves predictions…

CCHMM_PROF
Web

CCHMM_PROF

A hidden Markov model that exploits the information contained in multiple…

A hidden Markov model that exploits the information contained in multiple sequence alignments (profiles) to predict coiled-coil regions. CCHMM_PROF discriminates coiled-coil sequences with an…

LOGICOIL
Desktop
Web

LOGICOIL

Predicts the oligomeric state probabilities of a coiled-coil sequence. LOGICOIL…

Predicts the oligomeric state probabilities of a coiled-coil sequence. LOGICOIL currently allows to classify antiparallel dimers, parallel dimers, trimers and tetramers.

Socket
Desktop
Web

Socket

A software tool to identify coiled coils automatically in protein structures.…

A software tool to identify coiled coils automatically in protein structures. SOCKET unambiguously defines coiled-coil helix boundaries, oligomerisation states and helix orientations, and also…

SpiriCoil
Web

SpiriCoil

It is based on an approach to the coiled-coil prediction problem for coiled…

It is based on an approach to the coiled-coil prediction problem for coiled coils that fall into known superfamilies: hundreds of hidden Markov models representing coiled-coil-containing domain…

Multicoil
Desktop
Web

Multicoil

Predicts both the location and oligomerization state (two versus three helices)…

Predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 uses the flexibility of hidden Markov models (HMMs) in a Markov random…

pepcoil
Desktop

pepcoil

Predicts coiled coil regions in protein sequences. pepcoil calculates the…

Predicts coiled coil regions in protein sequences. pepcoil calculates the probability of a coiled-coil structure for windows of 28 residues through a protein sequence. It reads one or more sequences…

CCHMM
Web

CCHMM

Predictor of coiled-coil segments in proteins. A method based on hidden Markov…

Predictor of coiled-coil segments in proteins. A method based on hidden Markov models that complement the existing methods and outperforms them in the task of locating structurally-defined…

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