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CLePAPS: Fast Pair Alignment of Protein Structures Based on Conformational Letters  [PDF]
Sheng Wang,Wei-Mou Zheng
Quantitative Biology , 2007,
Abstract: Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes itself from other existing algorithms by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of the three angles formed by C_alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure similarity between any two such letters. CLePAPS regards an aligned fragment pair (AFP) as an ungapped string pair with a high sum of pairwise CLESUM scores. Using CLESUM scores as the similarity measure, CLePAPS searches for AFPs by simple string comparison. The transformation which best superimposes a highly similar AFP can be used to superimpose the structure pairs under comparison. A highly scored AFP which is consistent with several other AFPs determines an initial alignment. CLePAPS then joins consistent AFPs guided by their similarity scores to extend the alignment by several `zoom-in' iteration steps. A follow-up refinement produces the final alignment. CLePAPS does not implement dynamic programming. The utility of CLePAPS is tested on various protein structure pairs.
Letter
Laurenzi M
International Journal of Chronic Obstructive Pulmonary Disease , 2012, DOI: http://dx.doi.org/10.2147/COPD.S24686
Abstract: Letter Letter (2266) Total Article Views Authors: Laurenzi M Published Date January 2012 Volume 2012:7 Pages 33 - 34 DOI: http://dx.doi.org/10.2147/COPD.S24686 Received: 30 July 2011 Accepted: 01 August 2011 Published: 31 January 2012 Martino Laurenzi Senior Medical Director, Internal Medicine Medical Affairs, Forest Research Institute, Jersey City, NJ, USA The article “Optimizing management of chronic obstructive pulmonary disease in the upcoming decade” by Russell et al1 (January edition of the International Journal of Chronic Obstructive Pulmonary Disease) provides an overview of the pathophysiology of chronic obstructive pulmonary disease (COPD) and discusses emerging treatment options for managing this disease. I wish to draw your attention to the general information and clinical trial data presented on roflumilast. Several inaccuracies have been noticed in this section as well as in Table 2 of the article. View original paper by Russell and colleagues. Post to: Cannotea Citeulike Del.icio.us Facebook LinkedIn Twitter Readers of this article also read: Role of aliskiren in cardio-renal protection and use in hypertensives with multiple risk factors Long term results of a prospective randomized bilateral eye comparison trial of higher fluence, shorter duration ultraviolet A radiation, and riboflavin collagen cross linking for progressive keratoconus Iris and periocular adverse reactions to bimatoprost in Japanese patients with glaucoma or ocular hypertension Undertreatment of COPD: a retrospective analysis of US managed care and Medicare patients Bronchoscopic thermal vapor ablation in a canine model of emphysema Efficacy and safety characteristics of mometasone furoate/formoterol fumarate fixed-dose combination in subjects with moderate to very severe COPD: findings from pooled analysis of two randomized, 52-week placebo-controlled trials Efficacy and safety of a fixed-dose combination of mometasone furoate and formoterol fumarate in subjects with moderate to very severe COPD: results from a 52-week Phase III trial Insight into 144 patients with ocular vascular events during VEGF antagonist injections Evaluation of the surgical learning curve for I-125 episcleral plaque placement for the treatment of posterior uveal melanoma: a two decade review Letter to the editor
LETTER TO THE READER  [PDF]
Revista Eletr?nica de Educa??o , 2012,
Abstract: Letter to the Reader.
Editorial Letter  [cached]
Syed A.A. Rizvi
European Journal of Chemistry , 2011, DOI: 10.5155/eurjchem.2.1.ii-ii.433
Abstract: Editorial Letter
Letter to Editor  [PDF]
Anastasia Maggina
Open Journal of Accounting (OJAcct) , 2013, DOI: 10.4236/ojacct.2013.24013
Abstract: Letter to Editor
Letter to the Editor  [PDF]
Mirsad Hadzikadic
Open Journal of Modelling and Simulation (OJMSi) , 2014, DOI: 10.4236/ojmsi.2014.21002
Abstract: Letter to the Editor
Letter to the Editor  [PDF]
Md. Mamun Molla
Open Journal of Modelling and Simulation (OJMSi) , 2014, DOI: 10.4236/ojmsi.2014.21001
Abstract: Letter to the editor
Letter to Editor  [PDF]
Patrick Velte
Open Journal of Business and Management (OJBM) , 2014, DOI: 10.4236/ojbm.2014.21001
Abstract: Letter to Editor
Using profiles based on hydropathy properties to define essential regions for splicing  [PDF]
Anatoly Ivashchenko,Galina Boldina,Aizhan Turmagambetova,Mireille Régnier
Quantitative Biology , 2009,
Abstract: We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained 313 introns and 385 exons and were extracted from GenBank. They were used in order to define hydropathy profiles. Most human introns, around 99.66%, are likely to be U2- type introns. They have highly degenerate sequence motifs and many different sequences can function as U2-type splice sites. Our new profiles allow to identify regions which have conservative biochemical features that are essential for recognition by spliceosome. We have also found differences between hydropathy profiles for U2 or U12-types of introns on sets of spice sites extracted from SpliceRack database in order to distinguish GT?AG introns belonging to U2 and U12-types. Indeed, intron type cannot be simply determined by the dinucleotide termini. We show that there is a similarity of hydropathy profiles inside intron types. On the one hand, GT?AG and GC?AG introns belonging to U2-type have resembling hydropathy profiles as well as AT?AC and GT?AG introns belonging to U12-type. On the other hand, hydropathy profiles of U2 and U12-types GT?AG introns are completely different. Finally, we define and compute a pvalue; we compare our profiles with the profiles provided by a classical method, Pictogram.
Letter to the Editor  [PDF]
Lin Shi
Advances in Alzheimer's Disease (AAD) , 2013, DOI: 10.4236/aad.2013.23010
Abstract: Letter; Alzheimer’s Disease
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