GH11 xylanases: structure/function/properties relationships and applications

G Paës, JG Berrin, J Beaugrand - Biotechnology advances, 2012‏ - Elsevier
For technical, environmental and economical reasons, industrial demands for process-fitted
enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made …

Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016‏ - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

D Schneidman-Duhovny, M Hammel… - Nucleic acids …, 2016‏ - academic.oup.com
Abstract Small Angle X-ray Scattering (SAXS) is an increasingly common and useful
technique for structural characterization of molecules in solution. A SAXS experiment …

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

J Stourac, O Vavra, P Kokkonen, J Filipovic… - Nucleic acids …, 2019‏ - academic.oup.com
Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels,
and study of the ligands' transport through these transport pathways. Caver Web is the first …

Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier

L Orellana - Frontiers in molecular biosciences, 2019‏ - frontiersin.org
Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …

Motion planning algorithms for molecular simulations: A survey

I Al-Bluwi, T Siméon, J Cortés - Computer Science Review, 2012‏ - Elsevier
Motion planning is a fundamental problem in robotics that has motivated research since
more than three decades ago. A large variety of algorithms have been proposed to compute …

Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches

P Tuffery, P Derreumaux - Journal of The Royal Society …, 2012‏ - royalsocietypublishing.org
The recognition process between a protein and a partner represents a significant theoretical
challenge. In silico structure-based drug design carried out with nothing more than the three …

Visual analysis of biomolecular cavities: State of the art

M Krone, B Kozlíková, N Lindow… - Computer Graphics …, 2016‏ - Wiley Online Library
In this report we review and structure the branch of molecular visualization that is concerned
with the visual analysis of cavities in macromolecular protein structures. First the necessary …

Anticancer compound plumbagin and its molecular targets: a structural insight into the inhibitory mechanisms using computational approaches

MS Jamal, S Parveen, MA Beg, M Suhail… - PloS one, 2014‏ - journals.plos.org
Plumbagin (5-hydroxy-2-methyl-1, 4-naphthoquinone) is a naphthoquinone derivative from
the roots of plant Plumbago zeylanica and belongs to one of the largest and diverse groups …

Exploring the conformational states and rearrangements of Yarrowia lipolytica lipase

F Bordes, S Barbe, P Escalier, L Mourey, I André… - Biophysical journal, 2010‏ - cell.com
We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in
its closed conformation. The Lip2 structure is highly homologous to known structures of the …