[PDF] Top 20 SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information

... Results A new structural alphabet encoding: SAFlex Here we propose to extend the SA-based approach, HMM-SA ([ 3 , 15 ]) in SAFlex, to take into account 3D protein ... Voir le document complet

... Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function ...pathways and are now often targeted using small molecules for ... Voir le document complet

... of protein structure like secondary structures (Jones, 1999; Madera et ...2002), protein disorder (Madera et ...2010), protein flexibility (Bornot et ...of structural models (de ... Voir le document complet

... corresponding to one unique PDB (heteromers) or different PDB files corresponding 27 to a same protein in different conditions ...28 protein crystal structures contained 7,972 monomers ... Voir le document complet

... of protein structure like secondary structures (Jones, 1999; Madera et ...2002), protein disorder (Madera et ...2010), protein flexibility (Bornot et ...of structural models (de ... Voir le document complet

... bound and unbound forms, in terms of local ...thanks to a structural alphabet of 27 structural letters that allows a detailed description of the ...Using a control ... Voir le document complet

... assign a probability to each observation such that the moment conditions are satisfied (see Smith ...Back and Brown ...assigned to an observation for which the moment restrictions are not ... Voir le document complet

... reversibly and without a stable intermediate between the native and the unfolded states, have allowed re- searchers to establish the thermodynamic stability function accounting for the Gibbs ... Voir le document complet

... sensitivity and specificity of the profiles can be evaluated by the matchlist against the Swiss-Prot knowledgebase, which indicates the number of true positives, false positives and false negatives (Sigrist ... Voir le document complet

... Structural analyses Whereas the importance of charged amino acids for binding could be interpreted in terms of electrostatic interactions (see Introduction), the relevance of aromatic residues in limiting ... Voir le document complet

... assembly and disassembly in a process called ‘‘dynamic instability’’ ( Mitchison and Kirschner, 1984 ...Due to these intrinsic dynamics of the system, MTs have been difficult to study ... Voir le document complet

... of data by an SG project renders the conventional method of archiving and tracking experimental data via laboratory notebooks highly ...in structural biology because each step of the ... Voir le document complet

... Estrozi and Navaza, 2010). This revealed the negative stain volume of MaeΔ5 to comprise a double shell of density: an internal layer corresponding to the template, and an external one ... Voir le document complet

... A second input was added in the form of a different hydrophobicity profile - the reasoning being that hydrophobicity scales measured using different methodologies repres[r] ... Voir le document complet

... Unité de recherche INRIA Rhône-Alpes 655, avenue de l’Europe - 38330 Montbonnot-St-Martin France Unité de recherche INRIA Lorraine : LORIA, Technopôle de Nancy-Brabois - Campus scientifi[r] ... Voir le document complet

... deviance information criterion of Spiegelhalter et al. (2002) and the corresponding effective dimension allow for a wide range of interpretations and extensions outside exponential families, ... Voir le document complet

... assigned to the groups with maximal mass value by ECM and ...FCM and ECM the authors in the same detected group by FCM and ECM may have different ...us to detect the imprecise ... Voir le document complet

... attempted to reveal the relationship between local protein structure and its radiation ...Rao and Moller have investigated the appearance of protein carbon- ylation sites and ... Voir le document complet

... acid and these simple approaches have limitations (Yue et ...particular a major role in the kinetic ...designed a Src SH3 protein of 57 residues using an amino acid alphabet composed of ... Voir le document complet

... on a single machine, we did not consider any computational overhead of agents such as ...asynchronous and we consider the communication costs as unitary, thus irrelevant for the estimations of ... Voir le document complet