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BMCBI
2010
116views more  BMCBI 2010»
9 years 11 months ago
A hybrid approach to protein folding problem integrating constraint programming with local search
Background: The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy func...
Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel
BIOSYSTEMS
2008
83views more  BIOSYSTEMS 2008»
9 years 11 months ago
Hydrophobic condensation and modular assembly model of protein folding
Despite several decades of intense study, protein folding problem remains elusive. In this paper, we review current knowledge and the prevailing thinking in the field, and summari...
Tian-Yow Tsong, Chin-Kun Hu, Ming-Chya Wu
ISMB
1994
10 years 26 days ago
Inductive Logic Programming Used to Discover Topological Constraints in Protein Structures
Thispaperdescribesthe applicationof the Inductive Logic Programming0LP) program GOLEMto the discoveryof constraintsin the packingof beta-sheets in alpha/betaproteins. Theseconstra...
Ross D. King, Dominic A. Clark, Jack Shirazi, Mich...
BIOCOMP
2008
10 years 1 months ago
Inverse protein folding in 3D hexagonal prism lattice under HP model
Alireza Hadj Khodabakhshi, Ján Manuch, Aras...
BIRD
2008
Springer
109views Bioinformatics» more  BIRD 2008»
10 years 1 months ago
A Robust Class of Stable Proteins in the 2D HPC Model
The inverse protein folding problem is that of designing an amino acid sequence which has a prescribed native protein fold. This problem arises in drug design where a particular st...
Alireza Hadj Khodabakhshi, Ján Manuch, Aras...
BICOB
2010
Springer
10 years 4 months ago
Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications
Molecular dynamics simulations have been employed by biologists to study the protein folding problem. Such simulations have resulted in a large number of protein folding trajector...
Hui Yang, Saurabh Gupte, Runtang Wang, Rahul Parte
AI
2003
Springer
10 years 4 months ago
An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem
The prediction of a protein’s structure from its amino-acid sequence is one of the most important problems in computational biology. In the current focus on a widely studied abst...
Alena Shmygelska, Holger H. Hoos
ISNN
2004
Springer
10 years 4 months ago
Binary Input Encoding Strategy Based Neural Network for Globulin Protein Inter-residue Contacts Map Prediction
Abstract. Inter-residue contacts map prediction is one of the most important intermediate steps to the protein folding problem. In this paper, we focus on protein inter-residue con...
Guang-Zheng Zhang, De-Shuang Huang, Xin Huang
PPDP
2005
Springer
10 years 5 months ago
Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)
The paper describes a constraint-based solution to the protein folding problem on face-centered cubic lattices—a biologically meaningful approximation of the general protein fol...
Alessandro Dal Palù, Agostino Dovier, Enric...
ISAAC
2005
Springer
111views Algorithms» more  ISAAC 2005»
10 years 5 months ago
Multi-directional Width-Bounded Geometric Separator and Protein Folding
We introduce the concept of multi-directional width-bounded geometric separator and get improved separator for the grid graph, which improves exact algorithm for the protein foldin...
Bin Fu, Sorinel Adrian Oprisan, Lizhe Xu
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