Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and ...

The strategy for evaluating template-based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statisti...

The I-TASSER algorithm for 3D protein structure prediction was tested in CASP8, with the procedure fully automated in both the Server and Human sections. The quality of the server models is close to that of human ones but the human predictions incorporate more diverse templates from other servers which improve the human predictions in some of the distant homology targets. For the first time, th...

Given a protein sequence and the Cα coordinates on its backbone, the all-atom protein backbone reconstruction problem (PBRP) is to reconstruct the backbone by its 3D coordinates of N, C and O atoms. In the past few decades, many methods have been proposed for solving PBRP. Related research reveals that if proper prediction tools are selected to build the 3D coordinates of the desired atoms, the...

Given the primary sequence of a protein and its α-carbon coordinates, the allatom protein backbone reconstruction problem (PBRP) is to reconstruct the 3D coordinates of all atoms, including N, C, and O atoms on the backbone. A variety of methods for solving PBRP have been proposed, such as Adcock’s method, SABBAC, BBQ, and Chang’s methods. In this paper, we involve BBQ (Backbone Building from Q...

The role of chondrocytes in the development of infectious arthritis is not well understood. Several examples of mycoplasma-induced arthritis in animals indicate that chondrocytes come into direct contact with bacteria. The objective of this study was to analyze the interaction of an arthrogenic Mycoplasma synoviae strain WVU 1853 with chicken chondrocytes. We found that M. synoviae significantl...

OBJECTIVE To investigate the association between gastric cardia adenocarcinoma (GCA) and ten functional single nucleotide polymorphisms (SNPs), including TP53BP1 rs560191 G>C, CASP8 rs1035142 G>T, CASP7 rs3127075 G>C, CASP7 rs7907519 C>A, and six C1orf10/CRNN variants. We performed a hospital-based case-control study to evaluate the genetic effects of these SNPs. METHODS Two hundred and forty...

Recently, predicting proteins three-dimensional (3D) structure from its sequence information has made a significant progress due to the advances in computational techniques and the growth of experimental structures. However, selecting good models from a structural model pool is an important and challenging task in protein structure prediction. In this study, we present the first application of ...

PURPOSE Various genetic variants have been reported to be linked to an increased risk of meningioma. However, no confirmed conclusion has been obtained. The purpose of the study was to investigate potential meningioma-associated gene polymorphisms, based on published evidence. MATERIALS AND METHODS An updated meta-analysis was performed in September 2016. After electronic database searching a...