CAMPS

FH-cluster
FH-clusters are subclusters of SC-clusters (whereas each FH-cluster has exactly one parental SC-cluster). The abbreviation stands for functional homogeneous. Members of a FH-cluster have the same or similar domain architecture (i.e. the sequential order of domains) and are thus likely to have the same function.
Together with the MD-clusters, they form the second layer of the CAMPS database.

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Jalview
Jalview is a multiple alignment editor written in Java.

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MD-cluster
MD-clusters are subclusters of SC-clusters (whereas each MD-cluster has exactly one parental SC-cluster). The abbreviation stands for modeling distance. Members of a MD-cluster share a sequence identity of at least 30%.
Together with the FH-clusters, they form the second layer of the CAMPS database.

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Meta-model
A meta-model consists of a set of hidden Markov models each representing either a single transmembrane helix or a single loop region within a membrane protein. The individual submodels are connected to form one high-level model. The advantage of using meta-models is the possibility to combine topology, loop lengths and sequence similarity for the classification process. Meta-models are used in CAMPS to detect SC-clusters.

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SC-cluster
The SC-clusters form the first layer of the CAMPS database. The abbreviation stands for structurally correlated. Members of a SC-cluster are structurally homogeneous in terms of the variation of transmembrane helix number and loop lengths and are thus likely to share the same fold.
SC-clusters are further subdivided into FH-clusters and MD-clusters.

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Structural homogeneity
The structural homogeneity is calculated for each cluster and reflects the variation in the number of transmembrane helices (TMH) among the cluster members. It is defined as the ratio between the number of cluster members whose TMH number is within the TMH range of the cluster and the total number of members.

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TMH cores
Multiple alignments were created for selected members of each cluster. Based on these alignments, transmembrane helix (TMH) cores are defined as consecutive regions in the multiple alignment where 35% of the aligned sequences were predicted to be within a TMH.

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TMH range
In order to compensate for possible prediction errors and minor natural variation in transmembrane helix (TMH) number existing in protein families, a permissible range of TMH numbers, called TMH range, was defined for each cluster.
The TMH range is defined by the most common number of TMHs among the cluster members together with some minor deviations (e.g. if almost all cluster members have four TMHs, the TMH range is 3-5).

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Technische Universität München - Department of Genome Oriented Bioinformatics