Home  About us  Contact
 

Large Combinatorial Libraries (large + combinatorial_libraries)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

SmiLib v2.0: A Java-Based Tool for Rapid Combinatorial Library Enumeration

MOLECULAR INFORMATICS, Issue 3 2007
Andreas Schüller
Abstract An updated version of the SMILIB software tool for rapid combinatorial library enumeration was developed. SmiLib v2.0 offers the possibility to construct very large combinatorial libraries using the flexible and portable SMILES format. Libraries were created at rates of approximately 8,700,000 molecules per minute. Combinatorial building blocks are attached to scaffolds by means of linkers rather than to concatenate them directly. This allows for creation of customized libraries using linkers of different sizes and chemical nature. New features are: platform independence, correct handling of stereo chemistry, flexible reaction schemes, improved usability, a unique identifier for each molecule, the option to create libraries in SD format, a conformity check for SmiLib v2.0 SMILES notation restrictions, and decreased library enumeration times. SmiLib v2.0 is available as interactive graphical user interface application and command line tool. [source]

SMILIB: Rapid Assembly of Combinatorial Libraries in SMILES Notation

MOLECULAR INFORMATICS, Issue 7 2003
Andreas Schüller
Abstract A software tool was developed for fast combinatorial library enumeration (SMILIB). Its particular features are its simplicity to use, high flexibility in constructing combinatorial libraries and high speed of library construction. SMILIB offers the possibility to construct very large combinatorial libraries using the flexible and portable SMILES format. Libraries are generated at rates of approximately 30,000 molecules per minute. Combinatorial building blocks are attached to scaffolds by means of linkers rather than to concatenate them directly. This allows for creation of easily customized libraries using linkers of different size and chemical nature. A web interface for a limited web-based version of the software is available at URL: www.modlab.de. An unlimited binary version of SMILIB for command line execution on Linux systems is available from this URL. [source]

Stably folded de novo proteins from a designed combinatorial library

PROTEIN SCIENCE, Issue 1 2003
Yinan Wei
Abstract Binary patterning of polar and nonpolar amino acids has been used as the key design feature for constructing large combinatorial libraries of de novo proteins. Each position in a binary patterned sequence is designed explicitly to be either polar or nonpolar; however, the precise identities of these amino acids are varied extensively. The combinatorial underpinnings of the "binary code" strategy preclude explicit design of particular side chains at specified positions. Therefore, packing interactions cannot be specified a priori. To assess whether the binary code strategy can nonetheless produce well-folded de novo proteins, we constructed a second-generation library based upon a new structural scaffold designed to fold into 102-residue four-helix bundles. Characterization of five proteins chosen arbitrarily from this new library revealed that (1) all are ,-helical and quite stable; (2) four of the five contain an abundance of tertiary interactions indicative of well-ordered structures; and (3) one protein forms a well-folded structure with native-like features. The proteins from this new 102-residue library are substantially more stable and dramatically more native-like than those from an earlier binary patterned library of 74-residue sequences. These findings demonstrate that chain length is a crucial determinant of structural order in libraries of de novo four-helix bundles. Moreover, these results show that the binary code strategy,if applied to an appropriately designed structural scaffold,can generate large collections of stably folded and/or native-like proteins. [source]

Biosynthesis and Biological Screening of a Genetically Encoded Library Based on the Cyclotide MCoTI-I

CHEMBIOCHEM, Issue 16 2009
Jeffrey Austin
Cell-ing point: This study shows that MCoTI-cyclotides can provide an ideal scaffold for the biosynthesis of large combinatorial libraries inside living E. coli cells. Coupled to an appropriate in vivo reporter system, this library may rapidly be screened, for example, by fluorescence-activated cell sorting. [source]

Searching Combinatorial Libraries for Native Proteins with Novel Folds

CHEMBIOCHEM, Issue 9 2008
Jennifer L. Watkins
Shaping up: Discovering native proteins in large combinatorial libraries is a formidable challenge. Focused libraries composed of randomly distributed secondary structural elements can be used to rapidly identify amino acid sequences that adopt cooperatively folded structures. This approach holds great promise for exploring the diversity of protein shapes available to nature's set of structural elements. [source]