Getting a tree fast: Neighbor Joining, FastME, and distance-based methods [0.03%]
快速构建树：邻接连接、FastME 以及基于距离的方法
Richard Desper,Olivier Gascuel
Richard Desper
Neighbor Joining (NJ), FastME, and other distance-based programs including BIONJ, WEIGHBOR, and (to some extent) FITCH, are fast methods to build phylogenetic trees. This makes them particularly effective for large-scale studies or for boot...
Narayanan Eswar,Ben Webb,Marc A Marti-Renom et al.
Narayanan Eswar et al.
Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally de...
Liisa Holm,Sakari Kääriäinen,Chris Wilton et al.
Liisa Holm et al.
The Dali program is widely used for carrying out automatic comparisons of protein structures determined by X-ray crystallography or NMR. The most familiar version is the Dali server, which performs a database search comparing a query struct...
Gregory A Petsko
Gregory A Petsko
The underlying premise behind all attempts to determine a large number of diverse protein structures is that the total number of protein domain folds is much smaller, by many orders of magnitude, than the total number of sequences; in other...
Using Weeder for the discovery of conserved transcription factor binding sites [0.03%]
利用Weeder发现保守的转录因子结合位点
Giulio Pavesi,Graziano Pesole
Giulio Pavesi
One of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of motifs involved in the regulation ...
Using the Structure-function Linkage Database to characterize functional domains in enzymes [0.03%]
利用结构-功能连锁数据库表征酶的功能区
Shoshana Brown,Patricia Babbitt
Shoshana Brown
The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the...
Gary D Stormo
Gary D Stormo
This unit provides an overview of issues involved in domain recognition in protein and DNA sequences. It opens with a discussion of the two primary methods of domain representation, namely consensus sequences and alignment matrices (e.g., t...
Dimitris Dimitropoulos,John Ionides,Kim Henrick
Dimitris Dimitropoulos
The PDB ligand dictionary is the chemical reference database of all the small building block molecules (e.g., amino acids, nucleic acids, and bound ligands) in the Protein Data Bank (PDB) referenced by a distinct three-letter code identifie...
Using Pharmabase to perform pharmacological analyses of cell function [0.03%]
利用Pharmabase进行细胞功能药理学分析
Peter J S Smith,David Remsen
Peter J S Smith
Pharmabase is designed to form a bridge between the molecular dimension of cell transport processes and the functional manipulation of the protein players. It has as its emphasis membrane transport and related pharmacology. Several search a...
David H Mathews
David H Mathews
RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure under Microsoft Windows. This unit provides protocols for RNA secondary structure prediction and prediction of high-affinity oligonucleotide ...