Neural networks for determining protein specificity and multiple alignment of binding sites
Technical Report
·
OSTI ID:377143
- Hewlett-Packard Co., Loveland, CO (United States)
- Los Alamos National Lab., NM (United States)
- Univ. of Colorado, Boulder, CO (United States)
We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the equivalence of the method to maximizing Information Content of the aligned sites when simple models of the binding energy and the genome are employed. The network method subsumes those simple models and is capable of working with more complicated ones. This is demonstrated using a Markov model of the E. coli genome and a sampling method to approximate the partition function. A variation of Gibbs sampling aids in avoiding local minima.
- Research Organization:
- Stanford Univ., CA (United States)
- OSTI ID:
- 377143
- Report Number(s):
- CONF-9408117-; CNN: Grant HG00249; Grant ER61606; TRN: 96:005197-0023
- Resource Relation:
- Conference: 2. international conference on intelligent systems for molecular biology, Stanford, CA (United States), 15-17 Aug 1994; Other Information: PBD: [1994]; Related Information: Is Part Of Proceedings: Second international conference on intelligent systems for molecular biology; Altman, R.; Brutlag, D.; Karp, P.; Lathrop, R.; Searls, D. [eds.]; PB: 389 p.
- Country of Publication:
- United States
- Language:
- English
Similar Records
Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction
End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells
Journal Article
·
Sat Jun 03 00:00:00 EDT 2023
· Artificial Intelligence Chemistry
·
OSTI ID:377143
+4 more
End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
Journal Article
·
Thu Nov 10 00:00:00 EST 2022
· Bioinformatics
·
OSTI ID:377143
+7 more
Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells
Journal Article
·
Mon Jul 01 00:00:00 EDT 2013
· Developmental Cell
·
OSTI ID:377143
+4 more