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- Mahmood A Rashid, MA Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc Nghia Pham, Abdul Sattar
- BMC Bioinformatics
- 2013

Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic lattice for… (More)

Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino acids of the given protein. Local search algorithms can quickly find very good conformations by moving repeatedly from… (More)

Protein structure prediction is one of the most challenging problems in computational biology. Given a protein's amino acid sequence, a simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction energy among the amino acids. In this paper, we present a memory-based local search method for the simplified… (More)

Protein structure prediction is an unsolved problem in computational biology. One great difficulty is due to the unknown factors in the actual energy function. Moreover , the energy models available are often not very informative particularly when spatially similar structures are compared during search. We introduce several novel heuristics to augment the… (More)

- Swakkhar Shatabda, MA Hakim Newton, Mahmood A Rashid, Duc Nghia Pham, Abdul Sattar
- BMC Bioinformatics
- 2013

Given a protein's amino acid sequence, the protein structure prediction problem is to find a three dimensional structure that has the native energy level. For many decades, it has been one of the most challenging problems in computational biology. A simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction… (More)

Protein structure prediction is a challenging optimisation problem to the computer scientists. A large number of existing (meta-)heuristic search algorithms attempt to solve the problem by exploring possible structures and finding the one with minimum free energy. However, these algorithms often get stuck in local minima and thus perform poorly on large… (More)

Genome rearrangement algorithms are powerful tools to analyze gene orders in molecular evolution. Analysis of genomes evolving by reversals and transpositions leads to a combinatorial problem of sorting by reversals and transpositions, the problem of finding a shortest sequence of reversals and transpositions that sorts one genome into the other. In this… (More)

In this paper, we present a local search framework for lattice fit problem of proteins. Our algorithm significantly improves state-of-the-art results and justifies the significance of the lattice models. In addition to these, our analysis reveals the weakness of several energy functions used. A protein folds into a three dimensional native structure that… (More)

- Swakkhar Shatabda, M. A. Hakim Newton, Mahmood A. Rashid, Duc Nghia Pham, Abdul Sattar
- Adv. Bioinformatics
- 2014

Protein structure prediction (PSP) has been one of the most challenging problems in computational biology for several decades. The challenge is largely due to the complexity of the all-atomic details and the unknown nature of the energy function. Researchers have therefore used simplified energy models that consider interaction potentials only between the… (More)