Description Details Author(s) References
Functions to investigate the relation between biomolecular structures, their interactions, and the evolutionary information contained within sequence alignments of such molecules.
Package: | BioPhysConnectoR |
Version: | 1.6-7 |
Date: | 2011-11-03 |
Depends: | R (>= 2.11.0), snow, matrixcalc |
License: | GPL 2 |
Packaged: | 2010-23-09 13:50:31 UTC;weil |
Built: | R 2.12.1; x86_64-pc-linux-gnu; 2011-11-03 16:55:01 UTC; unix |
Index:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | aa2num Conversion of Amino Acids into Integer Values
BioPhysConnectoR-package BioPhysConnectoR
build.contacts Determine the Contact Map and Distance Matrices
build.hess Construct the Hessian Matrix
build.interact Compute the Interaction Matrix
build.invhess Compute the Covariance Matrix /
Inverse Hessian Matrix
extractPDB Extract Data from a PDB-File
fnorm Frobenius Norm of Two Matrices
get.bfacs Determine B factors
get.contact.list Returns a List of Contacts for a given Contact Map
get.cov Compute the Covariance Matrix /
Inverse Hessian Matrix
get.entropy Compute the Sequence Entropy for an Alignment
get.freqs Compute the Frequencies in an Alignment
get.mie Mutual Information
get.svd Singular Value Decomposition
lbpc List the Functions of the BioPhysConnectoR Package
mat.norm Normalisation of a Matrix
mat.read Read Matrix Data from a File
mat.sort Sort a Matrix According to a Specified Column
mat.write Writes Matrix Data to a File
read.fasta Reads aligned or un-aligned sequences from a FASTA format file
scpcp Self-Consistent Pair Contact Probability
Approximation
show.code Output of the Amino Acid Coding Scheme
sim Compute the Correlation Matrix and B Factors
for a List of PDBs
simc Computed Elastic Network Models for
Switched-Off-List of Contacts
sims Apply a List of Different Amino Acid Sequences
|
Franziska Hoffgaard <hoffgaard@bio.tu-darmstadt.de>, with contributions from Philipp Weil <weil@bio.tu-darmstadt.de> and Kay Hamacher <hamacher@bio.tu-darmstadt.de>
Maintainer: Franziska Hoffgaard <hoffgaard@bio.tu-darmstadt.de>
Hoffgaard, Weil, Hamacher (2010) BMC Bioinformatics 11, 199.
Hamacher (2006) Journal of Chemical Theory and Computation 2, 873–878.
Hamacher (2008) Gene 422, 30–36.
Hamacher (2009) Eur. Biophys. J., in press.
Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695–2696.
Tierney, Rossini, Li (2009) Int J Parallel Proc 37, 78–90.
Novomestky (2008) matrixcalc.
Newman (2002) Physical Review Letters 89, 208701-1 – 208701- 4.
Miyazawa, Jernigan (1996) Journal of Molecular Biology 256, 623–644.
Keskin, Bahar, Badretdinov, Ptitsyn, Jernigan (1998) Protein Science 7, 2578–2586.
Shannon (1948) The Bell System Technical Journal 27, 379–423
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