Insights into the role of electrostatics in temperature adaptation: a comparative study of psychrophilic, mesophilic, and thermophilic subtilisin-like serine proteases

Insights into the molecular mechanism underlying CD4-dependency and neutralization sensitivity of HIV-1: a comparative molecular dynamics study on gp120s from isolates with different phenotypes

(2018) Yi Li et al.   RSC Advances

Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

(2017) Peng Sang et al.   RSC Advances

Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study

(2017) Li-Quan Yang et al.   RSC Advances

Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations

(2016) Xing Du et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

(2015) Lin Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase

(2014) Lilja B. Jónsdóttir et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

(2014) Aoife C. Fogarty et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

(2014) Geir Villy Isaksen et al.   PLoS Computational Biology

The free energy landscape of protein folding and dynamics: a global view

(2013) Li-Quan Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

(2013) Li-Quan Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Soluble expression of proteins correlates with a lack of positively-charged surface

(2013) Pedro Chan et al.   Scientific Reports

Toward a Molecular Understanding of Protein Solubility: Increased Negative Surface Charge Correlates with Increased Solubility

(2012) Ryan M. Kramer et al.   BIOPHYSICAL JOURNAL

Insight Derived from Molecular Dynamics Simulation into Substrate-Induced Changes in Protein Motions of Proteinase K

(2012) Yan Tao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Is Stoichiometry-Driven Protein Folding Getting Out of Thermodynamic Control?

(2012) Xing-Lai Ji et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Comparison of homology models and crystal structures of cuticle-degrading proteases from nematophagous fungi: structural basis of nematicidal activity

(2011) Lianming Liang et al.   FASEB JOURNAL

The effect of calciums on molecular motions of proteinase K

(2010) Shu-Qun Liu et al.   JOURNAL OF MOLECULAR MODELING

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Comparison of anionic and cationic trypsinogens: The anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure

(2010) Annette Pasternak et al.   PROTEIN SCIENCE

Do salt bridges stabilize proteins? A continuum electrostatic analysis

(2010) Zachary S. Hendsch et al.   PROTEIN SCIENCE

Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K

(2009) Shu-Qun Liu et al.   JOURNAL OF MOLECULAR MODELING