Protein contact networks: an emerging paradigm in chemistry
Topology is at the very heart of chemistry. This stems from the fact that chemical thought,
since its prescientific alchemic origins, focused on the mutual relations between different …
since its prescientific alchemic origins, focused on the mutual relations between different …
A structural alphabet for local protein structures: improved prediction methods
C Etchebest, C Benros, S Hazout… - Proteins: Structure …, 2005 - Wiley Online Library
Three‐dimensional protein structures can be described with a library of 3D fragments that
define a structural alphabet. We have previously proposed such an alphabet, composed of …
define a structural alphabet. We have previously proposed such an alphabet, composed of …
Folding very short peptides using molecular dynamics
Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments
from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 …
from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 …
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
The noncoding genome plays an important role in de novo gene birth and in the emergence
of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the …
of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the …
Identification of function-associated loop motifs and application to protein function prediction
Motivation: The detection of function-related local 3D-motifs in protein structures can provide
insights towards protein function in absence of sequence or fold similarity. Protein loops are …
insights towards protein function in absence of sequence or fold similarity. Protein loops are …
Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures
A Pascual-García, D Abia, ÁR Ortiz… - PLoS Computational …, 2009 - journals.plos.org
Structural classifications of proteins assume the existence of the fold, which is an intrinsic
equivalence class of protein domains. Here, we test in which conditions such an …
equivalence class of protein domains. Here, we test in which conditions such an …
LEAP: Highly accurate prediction of protein loop conformations by integrating coarse‐grained sampling and optimized energy scores with all‐atom refinement of …
Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is
an unsolved problem. Its solution will significantly impact protein homology and template …
an unsolved problem. Its solution will significantly impact protein homology and template …
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
Background Structural genomics initiatives are producing increasing numbers of three-
dimensional (3D) structures for which there is little functional information. Structure-based …
dimensional (3D) structures for which there is little functional information. Structure-based …
Detecting protein candidate fragments using a structural alphabet profile comparison approach
Y Shen, G Picord, F Guyon, P Tuffery - PloS one, 2013 - journals.plos.org
Predicting accurate fragments from sequence has recently become a critical step for protein
structure modeling, as protein fragment assembly techniques are presently among the most …
structure modeling, as protein fragment assembly techniques are presently among the most …
“Pinning strategy”: a novel approach for predicting the backbone structure in terms of protein blocks from sequence
AG De Brevern, C Etchebest, C Benros, S Hazout - Journal of biosciences, 2007 - Springer
The description of protein 3D structures can be performed through a library of 3D fragments,
named a structural alphabet. Our structural alphabet is composed of 16 small protein …
named a structural alphabet. Our structural alphabet is composed of 16 small protein …