Published in Proteins on August 01, 2008
Data-driven prediction and design of bZIP coiled-coil interactions. PLoS Comput Biol (2015) 1.46
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
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J (2011) 1.39
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res (2010) 1.33
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
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins (2013) 1.20
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
GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res (2013) 1.06
Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med (2012) 1.04
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol (2010) 1.01
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. J Chem Theory Comput (2012) 1.00
De novo backbone scaffolds for protein design. Proteins (2010) 0.98
The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics (2013) 0.95
On human disease-causing amino acid variants: statistical study of sequence and structural patterns. Hum Mutat (2015) 0.93
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J Comput Chem (2011) 0.90
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. PLoS Comput Biol (2012) 0.89
Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. PLoS One (2014) 0.88
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit. J Am Chem Soc (2014) 0.87
Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method. J Chem Inf Model (2014) 0.86
Modeling large regions in proteins: applications to loops, termini, and folding. Protein Sci (2011) 0.86
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci (2014) 0.86
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PLoS One (2014) 0.86
Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys (2013) 0.84
AB-Bind: Antibody binding mutational database for computational affinity predictions. Protein Sci (2015) 0.84
Conformational sampling in template-free protein loop structure modeling: an overview. Comput Struct Biotechnol J (2013) 0.83
ProQ2: estimation of model accuracy implemented in Rosetta. Bioinformatics (2016) 0.83
Detecting protein-protein interactions with a novel matrix-based protein sequence representation and support vector machines. Biomed Res Int (2015) 0.82
DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC Bioinformatics (2016) 0.81
Protein structure prediction using residue- and fragment-environment potentials in CASP11. Proteins (2015) 0.81
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11. Proteins (2015) 0.81
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. Nucleic Acids Res (2011) 0.81
Modeling and molecular dynamics of the intrinsically disordered e7 proteins from high- and low-risk types of human papillomavirus. J Mol Model (2013) 0.81
Modeling proteins using a super-secondary structure library and NMR chemical shift information. Structure (2013) 0.79
STRUM: structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics (2016) 0.79
Refinement by shifting secondary structure elements improves sequence alignments. Proteins (2015) 0.79
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. Nucleic Acids Res (2016) 0.79
Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. Cell Cycle (2013) 0.78
Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. PLoS One (2014) 0.78
Protein NMR structures refined without NOE data. PLoS One (2014) 0.77
Protein structural model selection by combining consensus and single scoring methods. PLoS One (2013) 0.77
Detecting local residue environment similarity for recognizing near-native structure models. Proteins (2014) 0.77
ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep (2016) 0.77
Knowledge-based entropies improve the identification of native protein structures. Proc Natl Acad Sci U S A (2017) 0.76
Detecting protein conformational changes in interactions via scaling known structures. J Comput Biol (2013) 0.76
Using the unfolded state as the reference state improves the performance of statistical potentials. Biophys J (2012) 0.76
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics (2011) 0.75
Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption. Scientifica (Cairo) (2016) 0.75
GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking. Sci Rep (2016) 0.75
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? Algorithms Mol Biol (2013) 0.75
Heterologous expression of abaecin peptide from Apis mellifera in Pichia pastoris. Microb Cell Fact (2017) 0.75
On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding. PLoS One (2014) 0.75
StaRProtein, a web server for prediction of the stability of repeat proteins. PLoS One (2015) 0.75
Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement. Proc Congr Evol Comput (2014) 0.75
De Novo modeling of Envelope 2 protein of HCV isolated from Pakistani patient and epitopes prediction for vaccine development. J Transl Med (2014) 0.75
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures. BMC Bioinformatics (2014) 0.75
An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking. J Mol Model (2013) 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
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
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
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
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
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
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
Folding thermodynamics of model four-strand antiparallel beta-sheet proteins. Biophys J (2002) 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
Small open reading frames: current prediction techniques and future prospect. Curr Protein Pept Sci (2011) 0.84
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
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
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
Accurate single-sequence prediction of solvent accessible surface area using local and global features. Proteins (2014) 0.80
Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function. J Bioinform Comput Biol (2005) 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