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BioPhysConnectoR (version 1.6-8)

BioPhysConnectoR

Description

Utilities and functions to investigate the relation between biomolecular structures, their interactions, and the evolutionary information revealed in sequence alignments of these molecules.

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Version

Install

install.packages('BioPhysConnectoR')

Monthly Downloads

10

Version

1.6-8

License

GPL-2

Maintainer

Franziska Hoffgaard

Last Published

September 17th, 2012

Functions in BioPhysConnectoR (1.6-8)

sim

Compute the Covariance Matrices and B Factors for a List of PDBs
BioPhysConnectoR-package

BioPhysConnectoR
get.freqs

Compute the Frequencies in an Alignment
get.mie

Mutual Information
build.interact

Compute the Interaction Matrix
invhess

Compute the Covariance Matrix / Inverse Hessian Matrix
mat.sort

Sort a Matrix According to a Specified Column
show.code

Output of the Amino Acid Coding Scheme
extractPDB

Extract Data from a PDB-File
get.entropy

Compute the Sequence Entropy for an Alignment
mat.write

Writes Matrix Data to a File
get.svd

Singular Value Decomposition
simc

Computed Elastic Network Models for Switched-Off-List of Contacts
read.fasta

Read FASTA formated Sequences
mat.norm

Normalization of a Matrix
build.hess

Construct the Hessian Matrix
get.contact.list

Returns a List of Contacts for a given Contact Map
aa2num

Conversion of Amino Acids into Integer Values
get.bfacs

Determine B factors
lbpc

List the Functions of the BioPhysConnectoR Package
scpcp

Self-Consistent Pair Contact Probability Approximation
mat.read

Read Matrix Data from a File
build.contacts

Determine the Contact Map and Distance Matrices
sims

Apply a List of Different Amino Acid Sequences
fnorm

Frobenius Norm of Two Matrices