kpax.loria.fr
Kpax Protein Structure Alignmentprotein structure alignment, dynamic programming, kpax
http://kpax.loria.fr/
protein structure alignment, dynamic programming, kpax
http://kpax.loria.fr/
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Kpax Protein Structure Alignment | kpax.loria.fr Reviews
https://kpax.loria.fr
protein structure alignment, dynamic programming, kpax
kpax.loria.fr
Kpax Protein Structure Alignment
http://kpax.loria.fr/references.php
This article describes calculating multiple flexible alignments and the new "M-score" for scoring multiple alignments:. Calculating and scoring high quality multiple flexible protein structure alignments. DW Ritchie (2016). Bioinformatics. This article describes the original Kpax. Pair-wise structure alignment algorithm:. Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. 28(24) 3274-3281, and Supplementary Material. We thought that Kpax.
Kpax Protein Structure Alignment
http://kpax.loria.fr/datasets.php
Here is a collection of PDB files and simple shell scripts (some editing might be required) to superpose some "difficult" or "interesting" pairs of structures from the literature:. 05Mb) - 10 pairs from Fischer et al. (1996). 18Mb) - 19 pairs from Shatsky et al. (2002). 03Mb) - 6 pairs from Sippl and Wiederstein (2008). 06Mb) - 6 pairs from Gerstein and Levitt (1998). You can build Kpax. Databases of CATH and SCOP using these files (some editing required):. 1Kb), dir.cla.scop.txt 1.75.
Kpax Protein Structure Alignment
http://kpax.loria.fr/manual.php
Kpax User Manual - version 5.0.0. How Does it Work? What Can it Do? The Printed Results Table. Scoring Pair-wise and Multiple Alignments. Creating and Searching a User Database. Creating a CATH Database. Creating a SCOP Database. Controlling the PDB Output. Alignment and Superposition Parameters. Can also align and superpose unstructured peptides and peptide fragments. Additionally, Kpax. Is its great speed and robustness, which makes it especially well suited for searching structural databases such as C...
Kpax Protein Structure Alignment
http://kpax.loria.fr/download.php
Was developed for use on Linux workstations. It is not available for Windows or Mac systems. For Academic and Governmental users, a runtime version of Kpax. May be downloaded free of charge. Corporate users may also download the software for evaluation, although prior agreement with the author is required if the program is to be used for profit. Université de Lorraine.
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KBDOCK Server About Page
http://kbdock.loria.fr/about.php
A resource for knowledge-based protein docking. KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK extracts protein domain-domain interaction (DDI) and domain-peptide interaction (DPI) information from the PDB. Domain classification in order to analyse the spatial arrangements of DDIs and DPIs by Pfam family, and to propose structural templates for protein docking. Given a query Pfam domain, KBDOCK shows:. A Jmol view of th...
bioinformatics | Molecular Modelling
http://www.molecularmodelling.net/bioinformatics
Resources for Molecular Modelling. 8211; Gaussian based structural alignment. Theme created by PWT. Powered by WordPress.org.
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Kpax Protein Structure Alignment
Version 5.0.0 is now available! Version 5.0.0 can perform flexible structure alignments, multiple structure alignments, and multiple flexible structure alignments. It can also score alignments calculated by other programs, provided the alignment is given in a PIR or FASTA format file. Was developed by Dave Ritchie. Université de Lorraine.
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