Published in Proteins on February 01, 2004
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
A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol (2008) 1.62
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci (2004) 1.53
Bioinformatics for personal genome interpretation. Brief Bioinform (2012) 1.51
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics (2012) 1.49
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J (2011) 1.39
Contributions of hydrophobic domain interface interactions to the folding and stability of human gammaD-crystallin. Protein Sci (2005) 1.39
Sequence feature-based prediction of protein stability changes upon amino acid substitutions. BMC Genomics (2010) 1.13
The dependence of all-atom statistical potentials on structural training database. Biophys J (2004) 1.06
Causes of evolutionary rate variation among protein sites. Nat Rev Genet (2016) 1.03
Ultrafast hydration dynamics in protein unfolding: human serum albumin. Proc Natl Acad Sci U S A (2004) 0.99
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol (2006) 0.97
Prediction of B-cell epitopes using evolutionary information and propensity scales. BMC Bioinformatics (2013) 0.91
Stability and kinetic properties of C5-domain from myosin binding protein C and its mutants. Biophys J (2007) 0.80
Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction. Protein Sci (2008) 0.79
Adepth: New Representation and its implications for atomic depths of macromolecules. Nucleic Acids Res (2013) 0.78
Genetic Epidemiology of Glucose-6-Dehydrogenase Deficiency in the Arab World. Sci Rep (2016) 0.77
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. Protein Sci (2007) 0.77
Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials. Protein Sci (2009) 0.76
Fusogenic variants of a noncytopathic paramyxovirus. J Virol (2007) 0.76
A folding pathway-dependent score to recognize membrane proteins. PLoS One (2011) 0.76
A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function. Front Plant Sci (2016) 0.75
In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin. Adv Bioinformatics (2016) 0.75
Determinants of Thermostability in Serine Hydroxymethyltransferase Identified by Principal Component Analysis. Sci Rep (2017) 0.75
Influence of C-H...O interactions on the structural stability of β-lactamases. J Biol Phys (2013) 0.75
Analyzing pathogenic mutations of C5 domain from cardiac myosin binding protein C through MD simulations. Eur Biophys J (2008) 0.75
Focused Screening of ECM-Selective Adhesion Peptides on Cellulose-Bound Peptide Microarrays. Bioengineering (Basel) (2016) 0.75
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40
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
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins (2004) 1.60
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
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
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
A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins (2007) 1.05
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
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
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
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
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
QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins (2006) 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
Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins (2009) 0.89
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
Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins (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
Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction. Proteins (2010) 0.87
In-silico prediction of disorder content using hybrid sequence representation. BMC Bioinformatics (2011) 0.87
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
Improving computational protein design by using structure-derived sequence profile. Proteins (2010) 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
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
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
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
Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Hum Mol Genet (2014) 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
Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs. Biophys J (2002) 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
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
Refining near-native protein-protein docking decoys by local resampling and energy minimization. Proteins (2009) 0.79
The helix-coil transition revisited. Proteins (2007) 0.78
Domain graph of Arabidopsis proteome by comparative analysis. J Proteome Res (2005) 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
Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles. Proteins (2014) 0.75
The role of semidisorder in temperature adaptation of bacterial FlgM proteins. Biophys J (2013) 0.75
Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. Protein Sci (2012) 0.75