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Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.

eLife | Nov 2, 2016

Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block apoptosis in different cancers, we computationally designed three-helix bundle protein inhibitors specific for each BCL2 pro-survival protein. Following in vitro optimization, each inhibitor binds its target with high picomolar to low nanomolar affinity and at least 300-fold specificity. Expression of the designed inhibitors in human cancer cell lines revealed unique dependencies on BCL2 proteins for survival which could not be inferred from other BCL2 profiling methods. Our results show that designed inhibitors can be generated for each member of a closely-knit protein family to probe the importance of specific protein-protein interactions in complex biological processes.

Pubmed ID: 27805565 RIS Download

Mesh terms: Apoptosis | Computational Biology | Gene Expression Regulation, Neoplastic | Humans | Neoplasms | Protein Structure, Secondary | Proto-Oncogene Proteins c-bcl-2

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This is a list of tools and resources that we have found mentioned in this publication.


Coot

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

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Refmac

A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4.

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Phaser

Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.

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CCP4

Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure.

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ATCC

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

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Rosetta Biosoftware

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Following completion of the acquisition of Rosetta Biosoftware assets from Merck & Co., Inc. by Microsoft Corp. on June 26, 2009, Merck & Co., Inc. selected Ceiba Solutions, Inc (http://www.ceibasolutions.com) as the provider of product support for Rosetta Resolver, Elucidator and Syllego customers. Ceiba Solutions is a software and IT services company helping customers streamline and extend business processes through composite software development, application integration, and managed application services. Ceiba currently serves Life Science industry customers with outsourced managed services for R&D applications, as well as business software and integrated business processes. Ceiba Solutions is an active member of the Massachusetts Biotechnology Council and the BayBio Council. Ceiba Solutions has assumed complete responsibility for software maintenance and support associated with Rosetta Biosoftware product Licensees who are eligible for continued Technical Support and Software Upgrade Protection, and will retain that responsibility throughout the remainder of the 24 month Desupport Period.

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Rosetta

Software suite that includes algorithms for computational modeling and analysis of protein structures. It has enabled advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

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