DFS based partial pathways in GA for protein structure prediction
- Hoque, Md Tamjidul, Chetty, Madhu, Lewis, Andrew, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2008
- Type: Text , Conference paper
- Relation: Third IAPR International Conference, PRIB 2008
- Full Text:
- Reviewed:
- Description: Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2008
- Type: Text , Conference paper
- Relation: Third IAPR International Conference, PRIB 2008
- Full Text:
- Reviewed:
- Description: Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.
Extended HP model for protein structure prediction
- Hoque, Md Tamjidul, Chetty, Madhu, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Journal article
- Relation: Computational Biology and Bioinformatics Vol. Jan-Feb 2011, no. (2009 ), p. 234-245
- Full Text: false
- Reviewed:
- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
Genetic algorithm in ab initio protein structure prediction using low resolution model : a review
- Hoque, Md Tamjidul, Chetty, Madhu, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Book chapter
- Relation: Biomedical Data and Applications p. 317-342
- Full Text:
- Reviewed:
- Description: Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution.
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Book chapter
- Relation: Biomedical Data and Applications p. 317-342
- Full Text:
- Reviewed:
- Description: Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution.
Interactive effect of elevated CO2 and drought on physiological traits of Datura stramonium
- Javaid, Muhammad, Florentine, Singarayer, Mahmood, Athar, Wasaya, Allah, Javed, Talha, Sattar, Abdul, Sarwar, Naeem, Kalaji, Hazem, Ahmad, Hafiz, Worbel, Jacek, Ahmed, Mohammed, Telesiński, Arkadiusz, Mojski, Jacek
- Authors: Javaid, Muhammad , Florentine, Singarayer , Mahmood, Athar , Wasaya, Allah , Javed, Talha , Sattar, Abdul , Sarwar, Naeem , Kalaji, Hazem , Ahmad, Hafiz , Worbel, Jacek , Ahmed, Mohammed , Telesiński, Arkadiusz , Mojski, Jacek
- Date: 2022
- Type: Text , Journal article
- Relation: Frontiers in Plant Science Vol. 13, no. (2022), p.
- Full Text:
- Reviewed:
- Description: Rising atmospheric CO2 concentrations are known to influence the response of many plants under drought. This paper aimed to measure the leaf gas exchange, water use efficiency, carboxylation efficiency, and photosystem II (PS II) activity of Datura stramonium under progressive drought conditions, along with ambient conditions of 400 ppm (aCO2) and elevated conditions of 700 ppm (eCO2). Plants of D. stramonium were grown at 400 ppm and 700 ppm under 100 and 60% field capacity in a laboratory growth chamber. For 10 days at two-day intervals, photosynthesis rate, stomatal conductance, transpiration rate, intercellular CO2 concentration, water use efficiency, intrinsic water use efficiency, instantaneous carboxylation efficiency, PSII activity, electron transport rate, and photochemical quenching were measured. While drought stress had generally negative effects on the aforementioned physiological traits of D. stramonium, it was found that eCO2 concentration mitigated the adverse effects of drought and most of the physiological parameters were sustained with increasing drought duration when compared to that with aCO2. D. stramonium, which was grown under drought conditions, was re-watered on day 8 and indicated a partial recovery in all the parameters except maximum fluorescence, with this recovery being higher with eCO2 compared to aCO2. These results suggest that elevated CO2 mitigates the adverse growth effects of drought, thereby enhancing the adaptive mechanism of this weed by improving its water use efficiency. It is concluded that this weed has the potential to take advantage of climate change by increasing its competitiveness with other plants in drought-prone areas, suggesting that it could expand into new localities. Copyright © 2022 Javaid, Florentine, Mahmood, Wasaya, Javed, Sattar, Sarwar, Kalaji, Ahmad, Worbel, Ahmed, Telesiński and Mojski.
- Authors: Javaid, Muhammad , Florentine, Singarayer , Mahmood, Athar , Wasaya, Allah , Javed, Talha , Sattar, Abdul , Sarwar, Naeem , Kalaji, Hazem , Ahmad, Hafiz , Worbel, Jacek , Ahmed, Mohammed , Telesiński, Arkadiusz , Mojski, Jacek
- Date: 2022
- Type: Text , Journal article
- Relation: Frontiers in Plant Science Vol. 13, no. (2022), p.
- Full Text:
- Reviewed:
- Description: Rising atmospheric CO2 concentrations are known to influence the response of many plants under drought. This paper aimed to measure the leaf gas exchange, water use efficiency, carboxylation efficiency, and photosystem II (PS II) activity of Datura stramonium under progressive drought conditions, along with ambient conditions of 400 ppm (aCO2) and elevated conditions of 700 ppm (eCO2). Plants of D. stramonium were grown at 400 ppm and 700 ppm under 100 and 60% field capacity in a laboratory growth chamber. For 10 days at two-day intervals, photosynthesis rate, stomatal conductance, transpiration rate, intercellular CO2 concentration, water use efficiency, intrinsic water use efficiency, instantaneous carboxylation efficiency, PSII activity, electron transport rate, and photochemical quenching were measured. While drought stress had generally negative effects on the aforementioned physiological traits of D. stramonium, it was found that eCO2 concentration mitigated the adverse effects of drought and most of the physiological parameters were sustained with increasing drought duration when compared to that with aCO2. D. stramonium, which was grown under drought conditions, was re-watered on day 8 and indicated a partial recovery in all the parameters except maximum fluorescence, with this recovery being higher with eCO2 compared to aCO2. These results suggest that elevated CO2 mitigates the adverse growth effects of drought, thereby enhancing the adaptive mechanism of this weed by improving its water use efficiency. It is concluded that this weed has the potential to take advantage of climate change by increasing its competitiveness with other plants in drought-prone areas, suggesting that it could expand into new localities. Copyright © 2022 Javaid, Florentine, Mahmood, Wasaya, Javed, Sattar, Sarwar, Kalaji, Ahmad, Worbel, Ahmed, Telesiński and Mojski.
Photosynthetic activity and water use efficiency of Salvia verbenaca L. under elevated CO2 and water‐deficit conditions
- Javaid, Muhammad, Florentine, Singarayer, Ashraf, Muhammad, Mahmood, Athar, Sattar, Abdul, Wasaya, Allah, Li, Feng‐Min
- Authors: Javaid, Muhammad , Florentine, Singarayer , Ashraf, Muhammad , Mahmood, Athar , Sattar, Abdul , Wasaya, Allah , Li, Feng‐Min
- Date: 2022
- Type: Text , Journal article
- Relation: Journal of agronomy and crop science Vol. 208, no. 4 (2022), p. 536-551
- Full Text:
- Reviewed:
- Description: Investigating the combined effects of elevated CO2 concentration and water‐deficit on weed plants is crucial to gaining a thorough understanding of plant performance and modifying agricultural processes under changing climate conditions. This study examined the effect of elevated CO2 concentration and water‐deficit conditions on leaf gas exchange, water use efficiency, carboxylation efficiency and the photosystem II (PSII) activity of two Salvia verbenaca L., varieties. These varieties were grown under two CO2 concentrations (ambient conditions of 400 ppm and elevated conditions of 700 ppm) and two water regimes (well‐watered [100% field capacity] and water‐deficit conditions [60% field capacity]) in laboratory growth chambers. For 12 days, at 2‐day intervals, (i) leaf gas exchange parameters (photosynthesis rate, stomatal conductance, transpiration rate (E) and intercellular CO2 concentration (Ci)), (ii) water use efficiency (WUE), (iii) intrinsic water use efficiency (IWUE), (iv) instantaneous carboxylation efficiency and (v) PSII activity (fluorescence, quantum yield of PSII, photochemical efficiency of PSII, photochemical quenching and photosynthetic electron transport) were measured. Water‐deficit conditions had negative effects on studied parameters of both varieties, whereas elevated CO2 concentration had positive effects on the gas exchange, water use efficiency and PSII activity of both. Salvia verbenaca varieties grown under water‐deficit conditions from Day 0 to Day 5 showed a partial recovery in most of the parameters when the resumption of the well‐watered regime was reinstituted on Day 6. Salvia verbenaca varieties grown under water‐deficit conditions were re‐watered on day 6 and indicated a partial recovery in all the parameters. A comparison of the two varieties showed that var. vernalis recorded higher values of gas exchange, quantum yield of PSII and photochemical efficiency of PSII than var. verbenaca, but the water use efficiency of var. verbenaca was higher than that of var. vernalis. These differences serve to illustrate the complexity of such studies and suggest that a detailed understanding of the nature of weed infestations is essential if optimum management control is to be practiced. Elevated CO2 concentration mitigated the adverse effects of water‐deficit conditions and thereby enhanced the adaptive mechanism of this weed by improving its water use efficiency. It is thus likely that S. verbenaca has the potential to take advantage of climate change by increasing its relative competitiveness with other plants in drought‐prone areas, suggesting that it could significantly expand its invasive range under such conditions.
- Authors: Javaid, Muhammad , Florentine, Singarayer , Ashraf, Muhammad , Mahmood, Athar , Sattar, Abdul , Wasaya, Allah , Li, Feng‐Min
- Date: 2022
- Type: Text , Journal article
- Relation: Journal of agronomy and crop science Vol. 208, no. 4 (2022), p. 536-551
- Full Text:
- Reviewed:
- Description: Investigating the combined effects of elevated CO2 concentration and water‐deficit on weed plants is crucial to gaining a thorough understanding of plant performance and modifying agricultural processes under changing climate conditions. This study examined the effect of elevated CO2 concentration and water‐deficit conditions on leaf gas exchange, water use efficiency, carboxylation efficiency and the photosystem II (PSII) activity of two Salvia verbenaca L., varieties. These varieties were grown under two CO2 concentrations (ambient conditions of 400 ppm and elevated conditions of 700 ppm) and two water regimes (well‐watered [100% field capacity] and water‐deficit conditions [60% field capacity]) in laboratory growth chambers. For 12 days, at 2‐day intervals, (i) leaf gas exchange parameters (photosynthesis rate, stomatal conductance, transpiration rate (E) and intercellular CO2 concentration (Ci)), (ii) water use efficiency (WUE), (iii) intrinsic water use efficiency (IWUE), (iv) instantaneous carboxylation efficiency and (v) PSII activity (fluorescence, quantum yield of PSII, photochemical efficiency of PSII, photochemical quenching and photosynthetic electron transport) were measured. Water‐deficit conditions had negative effects on studied parameters of both varieties, whereas elevated CO2 concentration had positive effects on the gas exchange, water use efficiency and PSII activity of both. Salvia verbenaca varieties grown under water‐deficit conditions from Day 0 to Day 5 showed a partial recovery in most of the parameters when the resumption of the well‐watered regime was reinstituted on Day 6. Salvia verbenaca varieties grown under water‐deficit conditions were re‐watered on day 6 and indicated a partial recovery in all the parameters. A comparison of the two varieties showed that var. vernalis recorded higher values of gas exchange, quantum yield of PSII and photochemical efficiency of PSII than var. verbenaca, but the water use efficiency of var. verbenaca was higher than that of var. vernalis. These differences serve to illustrate the complexity of such studies and suggest that a detailed understanding of the nature of weed infestations is essential if optimum management control is to be practiced. Elevated CO2 concentration mitigated the adverse effects of water‐deficit conditions and thereby enhanced the adaptive mechanism of this weed by improving its water use efficiency. It is thus likely that S. verbenaca has the potential to take advantage of climate change by increasing its relative competitiveness with other plants in drought‐prone areas, suggesting that it could significantly expand its invasive range under such conditions.
Twin removal in genetic algorithms for protein structure prediction using low-resolution model
- Hoque, Md Tamjidul, Chetty, Madhu, Lewis, Andrew, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2011
- Type: Text , Journal article
- Relation: IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 8, no. 1 (2011), p. 234-245
- Full Text: false
- Reviewed:
- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
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