Renxiang Yan

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The lowest free-energy conformations are identified by structure clustering. A second round of assembly simulation is conducted, starting from the centroid models, to remove steric clashes and refine global topology. Final atomic structure models are constructed from the low-energy conformations by a two-step atomic-level energy minimization approach. The(More)
Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein(More)
A novel esterase gene (estSL3) was cloned from the Alkalibacterium sp. SL3, which was isolated from the sediment of soda lake Dabusu. The 636-bp full-length gene encodes a polypeptide of 211 amino acid residues that is closely related with putative GDSL family lipases from Alkalibacterium and Enterococcus. The gene was successfully expressed in E. coli, and(More)
G protein coupled receptors (GPCRs), also known as seven-transmembrane domain receptors, pass through the cellular membrane seven times and play diverse biological roles in the cells such as signaling, transporting of molecules and cell-cell communication. In this work, we develop a web server, namely the GPCRserver, which is capable of identifying GPCRs(More)
Protein three-dimensional (3D) structures provide insightful information in many fields of biology. One-dimensional properties derived from 3D structures such as secondary structure, residue solvent accessibility, residue depth and backbone torsion angles are helpful to protein function prediction, fold recognition and ab initio folding. Here, we predict(More)
Coiled coils are characteristic rope-like protein structures, constituted by one or more heptad repeats. Native coiled-coil structures play important roles in various biological processes, while the designed ones are widely employed in medicine and industry. To date, two major oligomeric states (i.e. dimeric and trimeric states) of a coiled-coil structure(More)
Locating the transmembrane regions of outer membrane proteins (OMPs) is highly important for deciphering their biological functions at both molecular and cellular levels. Here, we propose a novel method to predict the transmembrane regions of OMPs by employing the position- and composition-based features of sequence profiles. Furthermore, a simple(More)
IPv6, the successor of IPv4, has gotten a lot of investigation from the academic and research community as well as the manufacturers. Since it is coming near to commercialization, the deployment of IPv6 is becoming more and more urgent. One of the most appealing features in IPv6, stateless auto-configuration mechanism, can make the IPv6 terminal true "plug(More)
A novel multi-domain high molecular xylanase coding gene (xynSL3) was cloned from Alkalibacterium sp. SL3, an alkaliphilic bacterial strain isolated from the sediment of soda lake Dabusu. The deduced XynSL3 is composed of a putative signal peptide, three tandem domains of carbohydrate binding module (CBM) family 22, a catalytic domain of glycosyl hydrolase(More)
Protein S-sulfenylation (SOH) is a type of post-translational modification through the oxidation of cysteine thiols to sulfenic acids. It acts as a redox switch to modulate versatile cellular processes and plays important roles in signal transduction, protein folding and enzymatic catalysis. Reversible SOH is also a key component for maintaining redox(More)