Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 7924265

DATALOAD: a user-friendly program to prepare binding data for the "LIGAND" software.

J C Calvo
View original source ↗Export metadata ↓

Abstract

This paper presents a program for the preparation of binding data to be used with the LIGAND software. This program will analyze saturation and competition/displacement binding data, and prepare all the necessary files that provide the input values for the final processing by the LIGAND package. Features include choices of different units for specific activity of the labeled tracer, and screen editing of the data, and results are provided as an average of replicates or as individual points. The program creates a graphic file to observe the raw data as a B/T vs T graph, prior to the analysis with the LIGAND program. The program saves all the information in a session file. Calculation of the bound/free values for the raw data is also provided.

Explore related subjects

Computer GraphicsData Interpretation, StatisticalLigandsMathematical ComputingMicrocomputersModels, BiologicalProtein BindingRadioactive TracersRadioligand AssaySoftwareSoftware DesignUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

J C Calvo. 1994. DATALOAD: a user-friendly program to prepare binding data for the "LIGAND" software.. https://doi.org/10.1016/0010-4825(94)90016-7

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2000

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and as a by-product results in a 'morph movie'. We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an 'evolutionary morph'. Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of approximately 10 degrees and a maximum Calpha displacement of 17 A. Almost all involve at least one large torsion angle change of >140 degrees. The server is accessible at http://bioinfo.mbb.yale. edu/MolMovDB

Computer Graphics↗
PubMed2000

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.

Computer Graphics↗
PubMed2000

Keio Mutation Database (KMDB) for human disease gene mutations.

A database of mutations in human disease-causing genes has been constructed and named as Keio Mutation Database (KMDB). This KMDB utilizes a database software called MutationView which was designed to compile various mutation data and to provide graphical presentation of data analysis. Currently, the KMDB accommodates mutation data of 38 different genes for 35 different diseases which are involved in eye, heart, ear and brain. These KMDBs are accessible through http://mutview.dmb.med.keio.ac.jp with advanced internet browsers.

Computer Graphics↗