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We provide knowledge-based approaches to computational biology, bioinformatics, structural biology and chemogenomics. We license world class software on behalf of several renowned academic research groups and also offer contract research and consultancy services. Our experience is deep and we work with clients to tackle a variety of research challenges. If this approach strikes a chord, please contact us. Seaport World Trade Center. Meet Dr. Andrew Martin (University College London) author of abYsis.

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Home | chemogenomix.com Reviews

https://chemogenomix.com

We provide knowledge-based approaches to computational biology, bioinformatics, structural biology and chemogenomics. We license world class software on behalf of several renowned academic research groups and also offer contract research and consultancy services. Our experience is deep and we work with clients to tackle a variety of research challenges. If this approach strikes a chord, please contact us. Seaport World Trade Center. Meet Dr. Andrew Martin (University College London) author of abYsis.

INTERNAL PAGES

chemogenomix.com chemogenomix.com
1

Surfnet

http://www.chemogenomix.com/chemogenomix/Surfnet.html

Surface and void region detection. Surfnet was developed to calculate cleft, surfaces and void regions in proteins. It is a fairly simple program run from a parameter file. It is also use as a component of PDBsum Proprietary. Data input is from coordinate files the obey the PDB format. When Surfnet is run, output is written to an .srf file. This srf file can then be processed by the supporting tools to compare different sites. For visualisation a .den density file or VRML can be generated.

2

Abysis

http://www.chemogenomix.com/chemogenomix/Abysis.html

Central storage system for proprietary antibodies. Store and analyse sequences and 3D structures. Robust, automated, antibody numbering algorithms. Key tools for analysing frameworks, loops, humanness, atypical residues and more. Integrate your high value proprietary data with our robust statistical framework. Driven by proven abYsis. AbYsisProprietory allows users to perform all and more of the public version’s functions behind their own firewall. Integrated antibody sequence and structure analysis.

3

StrucAnalToolKit

http://www.chemogenomix.com/chemogenomix/StrucAnalToolKit.html

Perform Key operations on a 3D structure. Secondary Structure, Accessibility, Hydrogen bonds and Motifs. The Procheck suite calculates various core data including bond angles and lengths, torsion angles as well as properties such as secondary structure assignments, using the method described by Kabsch and Sander. IK McDonald and J.M. Thornton (1994) JMB 238:777-793. Satisfying Hydrogen Bonding Potential in Proteins. Beta and gamma turns. Helical geometry and interactions. Main Chain H bond diagram. Using...

4

Profit

http://www.chemogenomix.com/chemogenomix/Profit.html

After you have an alignment you will probably want to generate a superposition of your structures to view in 3D. ProFit was designed by Andrew Martin to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc. Some comments from users:. A user from Cambridge. A user from Los Alamos. A user from the University of Chicago.

5

CATHedral

http://www.chemogenomix.com/chemogenomix/CATHedral.html

Structure based sequence alignment using double dynamic programming. Pairwise and multiple alignments. When you have a either a new structure or an existing one that you wish to take forward as a drug discovery target it is sensible to first search the data base of know structures to find relevant similarities. For more information download this publication:. Three distantly related proteins osmolarity sensor protein (1byq) DNA gyrase (1z5a) and HSP90 (1byq) only have 10% residue identity over their enti...

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chemogenomix.com chemogenomix.com

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We provide knowledge-based approaches to computational biology, bioinformatics, structural biology and chemogenomics. We license world class software on behalf of several renowned academic research groups and also offer contract research and consultancy services. Our experience is deep and we work with clients to tackle a variety of research challenges. If this approach strikes a chord, please contact us. Seaport World Trade Center. Meet Dr. Andrew Martin (University College London) author of abYsis.

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