Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J Comput Chem. 2012; 33:2483- 91. [PubMed: 22847521]M. D. Tyka, K. Jung, D. Baker, Efficient sampling of protein conformational space using fast loop building and...
Protein structure prediction can be considered as a multimodal optimization problem for sampling the protein conformational space associated with an extremely complex energy landscape. To address this problem, a conformational space sampling method using multi-subpopulation differential evolution, MDE, is prop...
We present a method for constructing thousands of compact protein conformations from fragments and then connecting these structures to form a network of physically plausible folding pathways. This is the first attempt to merge the previous successes in fragment assembly methods with probabilistic roadmap...
Original Research Article DOI - 10.26479/2017.0302.08 DISTANCE GEOMETRY WITH IMPROVED SAMPLING OF CONFORMATIONAL SPACE FOR BIOMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY AND PROTEIN DESIGNProtein structure determination from experimental NMR spectroscopic data, Comparative Modeling and Protein Design ...
Nature only samples a small fraction of the sequence space that can fold into stable proteins. Furthermore, small structural variations in a single fold, sometimes only a few amino acids, can define a protein’s molecular function. Hence, to design proteins with novel functionalities, such as ...
Protein folding has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of quantum computing to solve a simplified version of protein folding. More precisely, we numerically investigate the per
Insulin and insulin-like growth factors I and II are closely related protein hormones. Their distinct evolution has resulted in different yet overlapping biological functions with insulin becoming a key regulator of metabolism, whereas insulin-like growth factors (IGF)-I/II are major growth factors....
Protein folding has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of quantum computing to solve a simplified version of protein folding. More precisely, we numerically investigate the per
The acute sensitivity to conformation exhibited by amide hydrogen exchange reactivity provides a valuable test for the physical accuracy of model ensembles developed to represent the Boltzmann distribution of the protein native state. A number of molecular dynamics studies of ubiquitin have predicted a we...
Given that computational resources is a key for handling complexes with a large number of subunits and also for computing a large number of protein complexes in a genome-scale study, finding a proper setting for sampling the conformation space is of the utmost importance. Our results show that ...