-
TOOLS FOR HOMOLOGY MODELING (COMPARATIVE MODELING)
Program Website address Program description
Geno3d http://pbil.ibcp.fr/ Automatic modeling of protein three-dimensional structure
Swiss Model http://www.expasy.org/swissmod/SWISS-MODEL.html An automated knowledge-based protein modeling server; first approach and optimise
CPHmodels Http://www.cbs.dtu.dk/services/CPHmodels/ Automated neural-network based protein modeling server
Modeller http://salilab.org/ A program for automated protein Homology Modeling
Amber http://amber.scripps.edu/ Similar package as CHARMm. Developed by Kollaman's group at UCSF
Homology http://www.accelrys.com/ Automatic Homology Modeling module. The software suite also has Modeller, SeqFold modules, Quanta
Wloop http://psb00.snv.jussieu.fr/wloop/ The Loop Homology Modeling Server
What-If Server http://www.cmbi.kun.nl/gv/servers/WIWWWI/ V.Friend's What-IF Homology Modeling Server
SPORulate http://cgat.ukm.my/spores/Predictory/sporulate/s_predict_metaserver.html Send jobs by 'SPORulation' (meta server)  to selected servers available above using the respective server's default values.
SDSC1 http://cl.sdsc.edu/hm.html SDSC Protein Structure Homology Modeling Server

Comments

Post a Comment

Popular posts from this blog

Multiple sequence alignment

-
Name Description Sequence Type* Alignment Type** Link Author Year License ABA A-Bruijn alignment Protein Global download B.Raphael  et al. 2004 Proprietary, without charge for educational, research and non profit. ALE manual alignment ; some software assistance Nucleotides Local download J. Blandy and K. Fogel 1994 (latest version 2007) GPL2 AMAP Sequence annealing Both Global server A. Schwartz and L. Pachter 2006 anon. fast, optimal alignment of three sequences using linear gap costs Nucleotides Global paper   software D. Powell, L. Allison and T. I. Dix 2000 BAli-Phy Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation Both Global WWW+download BD Redelings and MA Suchard 2005 (latest version 2015) GPL Base-By-Base Java-based multiple sequence alignment editor with integrated analysis tools Both Local or Global download R. Brodie  et al. 2004 Free, requires registration. CHAOS/DIALIGN Iterative alignment Both Local (preferred) ...
Read more

Pairwise alignment

-
Name Description Sequence Type* Alignment Type** Link Author Year ACANA fast heuristic anchor based pairwise alignment Both Both download Huang, Umbach, Li 2005 AlignMe Alignments for membrane protein sequences Protein Both download , server M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest 2013 Bioconductor Biostrings::pairwiseAlignment Dynamic programming Both Both + Ends-free site P. Aboyoun 2008 BioPerl  dpAlign Dynamic programming Both Both + Ends-free site Y. M. Chan 2003 BLASTZ,LASTZ Seeded pattern-matching Nucleotide Local download , download Schwartz  et al. [9] [10] 2004,2009 DNADot Web-based dot-plot tool Nucleotide Global server R. Bowen 1998 DOTLET Java-based dot-plot tool Both Global applet M. Pagni and T. Junier 1998 FEAST Posterior based local extension with descriptive evolution model Nucleotide Local site A. K. Hudek and D. G. Brown 2010 G-PAS GPU-based dynamic programming with backtracking Both Local, SemiGlobal, Global site+download W. Fr...
Read more

5 Projects completed by Aditya Jain

-
Image
1. An integrated Repository of Computational Prediction of Deleterious SNPs Involved in Pathway of Bacterial Invasion of Epithelial Cells (BIoEC) in Homo sapiens Oct 2014 – Oct 2014 Project description polyBIoECP is a directory of all the synonymous (sSNP) and non synonymous (nsSNP) polymorphisms collected using SCAN database which are associated with various genes involved in bacterial invasion of epithelial cells pathway. Â It is an effort to evaluate the phenotypic effect of all known nsSNPs of the genes involved in BIoEC pathway and to enable researchers an easy access. To further validate, this database was developed with an updated list of all validated nsSNPs from dbSNP (NCBI) and their effect on the structure and functions of the proteins along with their genomic elements such as miRNA, CNV and CpG islands. BIoECP also has a comparative analysis of native and mutant protein (using MODELLER) of the respective polymorphism validated using Ramachandran Plot. Other...
Read more