Homology modeling and valence mapping have been used to predict the location and structure of Na(+) and K(+) binding sites in the Na(+)-K(+)-ATPase on the basis of the known atomic resolution structure of SERCA. Additional sites are predicted that may be associated with intracellular access and extracellular egress pathways for Na(+). The model predictions are in excellent agreement with previo...

An alternative treatment for staphylococcal infections caused by antibiotic-resistance strains is to lyse staphylococci with peptidoglycan hydrolases, for example, a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP). Here, CHAPs were analyzed in 12 Staphylococcus aureus genomes and 44 staphylococcal phage genomes. There are 234 putative CHAP-containing proteins and only 64 non-ident...

The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy functi...

We had participated in the CASP4 (Fourth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction) that is the competition of the protein structure prediction in 2000 [3]. Our server were estimated almost the best in the CAFASP2 (Critical Assessment of Fully Automated Structure Prediction) that is the full automatic homology modeling section of CASP4 [...

This study is a user report on modeling and predicting the F0 contour of Japanese utterances with PENTA Model and AM Theory. Through a 2640-word corpus of Japanese, the two models were compared using two versions of PENTAtrainer, as well as newly developed AMtrainer, respectively. The respective modelling and synthesis accuracies of different models are discussed with reference to the type of i...

Different procedures for obtaining homology models for P450s are investigated using various sequence alignments sharing various levels of sequence identity with available P450 crystal structures. In this analysis, we have investigated how well homology modeling can reproduce known crystal structures as well as how effectively these homology models can be used to reproduce known ligand-binding m...

In a recent article (1), Trifonov has developed an approach, conceptually inspired by principal component analysis (PCA), for arriving at a consensus definition of “life” as “self-reproduction with variations”. In appreciation of the sound analytical effort applied rigorously on a comprehensive body of literature, I will refer to both the approach and the definition as “Trifonovian”. The Trifon...

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduce...