Published in Proteins on August 01, 2009
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RosettaDock in CAPRI rounds 6-12. Proteins (2007) 1.08
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Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins (2005) 1.00
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Inherent limitations in protein-protein docking procedures. Bioinformatics (2006) 0.94
Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics (2005) 0.92
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins (2005) 0.92
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Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72
Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins (2004) 2.16
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (2011) 2.13
Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins (2008) 1.81
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem (2005) 1.76
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci (2004) 1.74
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Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network. Proteins (2009) 1.59
Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins (2007) 1.57
SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem (2011) 1.57
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci (2004) 1.53
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics (2005) 1.52
Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties. Proteins (2007) 1.45
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci (2008) 1.45
SPARKS 2 and SP3 servers in CASP6. Proteins (2005) 1.43
A strategy for the proliferation of Ulva prolifera, main causative species of green tides, with formation of sporangia by fragmentation. PLoS One (2010) 1.42
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins (2007) 1.39
Folding rate prediction using total contact distance. Biophys J (2002) 1.37
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res (2010) 1.33
SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn (2012) 1.32
Quantifying the effect of burial of amino acid residues on protein stability. Proteins (2004) 1.29
SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS One (2008) 1.27
Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure (2009) 1.23
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics (2010) 1.21
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci (2003) 1.17
DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci (2007) 1.14
Real-value prediction of backbone torsion angles. Proteins (2008) 1.10
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins (2002) 1.08
Structural insights into the histone H1-nucleosome complex. Proc Natl Acad Sci U S A (2013) 1.08
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins (2009) 1.07
The dependence of all-atom statistical potentials on structural training database. Biophys J (2004) 1.06
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DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol (2013) 1.02
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins (2005) 1.00
BEST: improved prediction of B-cell epitopes from antigen sequences. PLoS One (2012) 0.99
Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics (2011) 0.99
A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins (2012) 0.99
Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. Biophys J (2004) 0.99
PSI-driven cyclic electron flow allows intertidal macro-algae Ulva sp. (Chlorophyta) to survive in desiccated conditions. Plant Cell Physiol (2011) 0.99
Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry (2009) 0.99
Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biol (2011) 0.99
Critical nucleation size in the folding of small apparently two-state proteins. Protein Sci (2004) 0.98
Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model. Biophys J (2007) 0.97
Predicting residue-residue contact maps by a two-layer, integrated neural-network method. Proteins (2009) 0.97
SCUD: fast structure clustering of decoys using reference state to remove overall rotation. J Comput Chem (2005) 0.96
An economic assessment of astaxanthin production by large scale cultivation of Haematococcus pluvialis. Biotechnol Adv (2011) 0.95
QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins (2006) 0.95
Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. J Chem Phys (2008) 0.95
Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. J Mol Biol (2011) 0.91
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J Comput Chem (2011) 0.90
The Bryopsis hypnoides plastid genome: multimeric forms and complete nucleotide sequence. PLoS One (2011) 0.90
Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins (2009) 0.89
Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins (2008) 0.88
Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. J Chem Phys (2008) 0.88
LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains. J Comput Chem (2013) 0.87
The enhancement of cyclic electron flow around photosystem I improves the recovery of severely desiccated Porphyra yezoensis (Bangiales, Rhodophyta). J Exp Bot (2012) 0.87
In-silico prediction of disorder content using hybrid sequence representation. BMC Bioinformatics (2011) 0.87
Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction. Proteins (2010) 0.87
Differential expression of rubisco in sporophytes and gametophytes of some marine macroalgae. PLoS One (2011) 0.86
Improving computational protein design by using structure-derived sequence profile. Proteins (2010) 0.86
Prediction of RNA binding proteins comes of age from low resolution to high resolution. Mol Biosyst (2013) 0.86
Thermodynamics and stability of a beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. Protein Sci (2004) 0.86
Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome. Proteins (2013) 0.86
Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. J Proteome Res (2006) 0.85
Intrinsically semi-disordered state and its role in induced folding and protein aggregation. Cell Biochem Biophys (2013) 0.85
Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys (2013) 0.84
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J Comput Chem (2014) 0.84
Folding thermodynamics of model four-strand antiparallel beta-sheet proteins. Biophys J (2002) 0.84
Small open reading frames: current prediction techniques and future prospect. Curr Protein Pept Sci (2011) 0.84
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations. Nucleic Acids Res (2005) 0.83
The dual role of a loop with low loop contact distance in folding and domain swapping. Protein Sci (2002) 0.83
Trends in template/fragment-free protein structure prediction. Theor Chem Acc (2010) 0.83
Design and folding of a multidomain protein. Biochemistry (2005) 0.83
Protein flexibility prediction by an all-atom mean-field statistical theory. Protein Sci (2005) 0.82
Comparison of chlorophyll and photosynthesis parameters of floating and attached Ulva prolifera. J Integr Plant Biol (2010) 0.82
Comparison of different cells of Haematococcus pluvialis reveals an extensive acclimation mechanism during its aging process: from a perspective of photosynthesis. PLoS One (2013) 0.81
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Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs. Biophys J (2002) 0.81
SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. Methods Mol Biol (2014) 0.81
Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models. IEEE Trans Nanobioscience (2015) 0.81
Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function. J Bioinform Comput Biol (2005) 0.80
Accurate single-sequence prediction of solvent accessible surface area using local and global features. Proteins (2014) 0.80
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J Comput Chem (2014) 0.80
Hydrogen production of a salt tolerant strain Bacillus sp. B2 from marine intertidal sludge. World J Microbiol Biotechnol (2011) 0.79
Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes. Hum Mol Genet (2006) 0.79
The physiological links of the increased photosystem II activity in moderately desiccated Porphyra haitanensis (Bangiales, Rhodophyta) to the cyclic electron flow during desiccation and re-hydration. Photosynth Res (2013) 0.79
The helix-coil transition revisited. Proteins (2007) 0.78
Development of a PNA probe for fluorescence in situ hybridization detection of Prorocentrum donghaiense. PLoS One (2011) 0.78
Computational prediction of microRNAs and their targets from three unicellular algae species with complete genome sequences. Can J Microbiol (2011) 0.78
Screening and hydrogen-producing characters of a highly efficient H₂-producing mutant of Rhodovulum sulfidophilum P5. Bioresour Technol (2013) 0.78
Comparative Analysis of MicroRNAs between Sporophyte and Gametophyte of Porphyra yezoensis. Comp Funct Genomics (2012) 0.77
Domain graph of Arabidopsis proteome by comparative analysis. J Proteome Res (2005) 0.77
Desiccation enhances phosphorylation of PSII and affects the distribution of protein complexes in the thylakoid membrane. Physiol Plant (2014) 0.77
Photosystem I shows a higher tolerance to sorbitol-induced osmotic stress than photosystem II in the intertidal macro-algae Ulva prolifera (Chlorophyta). Physiol Plant (2014) 0.77
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform (2016) 0.77
Machine learning models in protein bioinformatics. Curr Protein Pept Sci (2011) 0.76