SOFT WARE ON PROTEIN蛋白质分析软件

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1 AnthePro 6.0 7 g$ I8 _0 [: w5 S, O
软件大小： 52,570K. o1 g! F- W( p: H/ K
软件语言： 英文
) P  d/ B+ A$ ~$ l6 u软件类别： 蛋白质分析软件类
* H* e  f, \2 W5 q. Y运行环境： Win9x/Me/NT/2000/XP/2003
7 H; t) ]4 }/ _加入时间： 2009-5-6
5 F! ^! }) z8 K/ H! m1 V原始网站： Home Page
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ANTHEPROT (ANalyse THE PROTeins) is the result of about 10 years of biocomputing activity of a group of the Institute of Biology and Chemistry of Proteins. The main idea was to integrate into a single package most of the methods designed for protein sequence analysis.
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/ o; ^, {5 L% }3 D$ I, F蛋白序列分析软件包ANTHEPROT 5.0，包括了蛋白质研究领域所包括的大多数内容。应用此软件包，使用个人电脑，便能进行各种蛋白序列分析与特性预测,包括：进行蛋白序列二级结构预测；在蛋白序列中查找符合PROSITES数据库的特征序列；绘制出蛋白序列的所有理化特性曲线；在Internet或本地蛋白序列数据库中查找类似序列；计算蛋白序列分子量，比重与各蛋白残基百分组成；计算蛋白序列滴定曲线与等电点；选定一个片段后，绘制Helical Wheel图；进行点阵图（Dot Plot）分析；计算信号肽潜在的断裂位点等功能。' m% ]9 V+ w: w- z
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   中文使用介绍 122K,希望对大家的使用有所帮助。 2 x) L/ O- z/ M: p" S! a7 j+ ^4 I% q

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2 PSAAM( B3 r5 R+ Z* A
软件大小： 390KB & s7 W! T6 ]3 e
软件语言： 英文
0 {9 c) |4 ~* r, u3 o: D# ^. ?# x软件类别： 蛋白质分析软件类
' L" K! ?# u8 y# ], ]9 M% m4 x运行环境： Win9x/Me/NT/2000/XP/2003
0 Q3 `% v' G9 {+ e0 R( E加入时间： 2006-8-16
. {& X: P- F8 U原始网站： Home Page# L% c( Y' N! q$ b! _3 n1 h% J; f
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We have developed a number of programs to aid in the Protein Sequence Analysis And Modelling (PSAAM). The package contains a main program (PSAAM), and several ancillary programs (INFORMAT, calculates mean sequence profiles and mutability moment (conservation moment) from aligned sequences; FINDSEQ, will find sequence strings (structural motifs, binding domains, etc.) in a sequence file, or a directory of sequence files; GENBANK, will extract sequence data from a file saved from Entrez).+ D& f, M  ~6 J/ i+ Q$ P1 A5 _& \/ I
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The main PSAAM program includes many useful features for analysis of structural information from sequence data, cartoons for graphical representation of secondary structures, prediction programs, and prediction aids, a ribosome function for generation of coordinates sets in PDB format (including Header information) for viewing by molecular graphics packages (examples, see also PDVWIN), and a SeqPlot function for plotting secondary structural models (helical cylinders and wheels, coils, etc., with each residue indicated by a circle, color-coded (or coded by line thickness) according to the current physico-chemical index. This latter function can be used to make "helical cylinder models".
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* X* f; q: t8 }' t: {蛋白质序列分析软件包。1 s8 k% Q# y8 o  i' F+ b

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3 VHMPT
: f/ I. P& V7 v5 P& q. [4 j软件大小： 762K
* Q( a$ I- h0 ]软件语言： 英文
# D% i3 K5 c* }' r- f软件类别： 蛋白质分析软件类
- P( D6 y, ?. J运行环境： Win9x/Me/NT/2000/XP/2003 6 Y- i' b3 q; ?. L5 j5 v4 F6 K
加入时间： 2009-5-64 I* f, K/ z4 p: D9 \  O' ]* m  f
原始网站： Home Page
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VHMPT is a graphical Viewer and editor for Helical Membrane Protein Topologies. It is a program that can automatically generate a schematic 2D topology for a protein with transmembrane helices; the input requires only the protein's amino acid sequence and sequence range of its helices. Through an interactive graphical interface, VHMPT allows users to modify layout of the generated topology, as well as annotate with arrows and texts. In addition, with a multiple-sequence alignment, VHMPT can color-code the degree of conservation for each of the aligned amino acids, thus highly conserved (or variable) amino acids or topology regions of the interested protein can be readily recognized and visualized in contrasting colors.1 i8 @! q; Q% B4 z5 m' O- ~

0 f0 x$ u4 s. A3 Q1 ?' r. CVHMPT（Viewer and editor for Helical Membrane Protein Topologies）是螺旋状膜蛋白拓扑结构观察与编辑软件，可以自动生成带有跨膜螺旋的蛋白的示意性2维拓扑结构，并可对拓扑结构进行交互编辑。由台湾生物医学科学研究所的黄明经博士编制。安装Tcl 8.0 (7M)方可运行。

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4 MPEx 3.0) K+ e. j2 v" @
软件大小： 2000KB
4 H! c2 G8 {# V) ]4 T+ K软件语言： 英文
: R6 k0 c1 T2 V4 w  k软件类别： 蛋白质分析软件类
& l: [: l& R( Z* H: f运行环境： Win9x/Me/NT/2000/XP/2003
( }- p, r0 [* H! }6 z. Y4 r加入时间： 2007-8-211 b, B* r; W7 J6 v
原始网站： Home Page
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- x# S. B5 V1 L6 ZMembrane Protein Explorer (MPEx), a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic principles. Click on the Java applet button at right to start MPEx. For instructions, see Features at a Glance and Brief Instructions for MPEx below, or the full documentation. Current version: 3.0. MPEx can also be installed on your computer as a Web Start application. A useful adjunct to MPEx is MPtopo, a database of Membrane Protein topology accessible from MPEx.
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（Membrane Protein Explorer）研究膜蛋白拓扑学结构和其它特性的JAVA软件。软件可以很方便地使用膜蛋白拓扑结构数据库MPtopo,（a database of Membrane Protein topology）。需要JAVA运行环境。软件已经不提供单机版，可直接到该网站点击运行。

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5 Osprey 1.2.0+ s! ~) I- O( D! H
软件大小： 21900KB + x* g- F7 t2 g' Y+ `$ m- r
软件语言： 英文 ) B" [, }, O3 @
软件类别： 蛋白质分析软件类
* L" f" y+ q2 s% h; b  J+ q运行环境： Win9x/Me/NT/2000/XP/2003 . o, u% ^; ?) U6 A  ^0 m4 v" E" @2 K
加入时间： 2006-8-167 j5 w* Z* S% S( E- O1 M1 d' M$ ?
原始网站： Home Page
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The Osprey Network Visualization System is a tool for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods. ! `# Y- l" `/ k, G: Q

! ?; u% _) _" O, W' Z5 M蛋白质相互作用网络可视化系统。是加拿大多伦多大学一个生物信息学研究组开发的，目的在于更好的研究蛋白质相互作用网络(protein-protein interaction networks)和蛋白质复合物。软件本身和(BIND,GRID)数据库整合，涉及到蛋白质、核酸序列又和GenBank交叉链接。使用手册，4.7M，PDF格式。
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Thank you for sharing

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6 InterViewer 4.0
4 \7 y2 f* c& m) Q  J( U7 E软件大小： 760KB
& {. ], A& ]; A& r, ]软件语言： 英文 * o. a: @! V, V2 W0 G
软件类别： 蛋白质分析软件类
8 B  |" S+ x8 z7 _2 L运行环境： Win9x/Me/NT/2000/XP/2003 ) n- G5 N2 _8 d& ~! D' T
加入时间： 2006-8-16# G! u+ g1 B3 u# U, H3 {/ v2 \! t; Y- Y  N
原始网站： Home Page
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Protein-protein interaction networks often consist of thousands of nodes or more, which severely limit the usefulness of many graph drawing tools because they become too slow for interactive anal- ysis of the networks and because they produce cluttered drawings with many edge crossings. We present a new, extremely fast layout algorithm and its implementation called InterViewer3 for visualizing large-scale protein interaction networks. InterViewer3 (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer3 over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.% j+ |& M4 y! d' o

# K8 Z9 C: X3 F5 Z2 Y显示和分析蛋白交互作用软件，据其网站介绍，运行速度比其他软件快许多。0 B4 v6 J) w7 v( _+ y' K

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7 Fiter 1.01 a( J& S% R" u0 A% ~1 P
软件大小： 25K8 o2 d1 j. d4 q. D' k1 [  }8 {
软件语言： 中文
4 \$ ~; y1 \4 |6 v软件类别： 蛋白质分析软件类
# y' ?* G& O; M- ^+ Y运行环境： Win9x/Me/NT/2000/XP/2003 2 M; z1 T" {6 \+ T" ?) {/ E
加入时间： 2008-8-12
( K. z. c" S8 c- @- i原始网站： Home Page
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本免费中文软件可以对蛋白质的MALDI-TOF分析结果数据（其它数据作者未做测试）进行角蛋白、牛胰蛋白和猪胰蛋白自切峰的滤除，也可对自定义任意数据进行滤除。角蛋白、牛胰蛋白和猪胰蛋白自切峰由NCBA提供。由作者杨亮和霍晨敏授权生物软件网发布。软件运行需要先安装微软的.net framework，23M。简单使用说明，200K。
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