Yaoqi Zhou
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Computer Science
Yaoqi Zhou's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
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(Suggest an Edit or Addition)Yaoqi Zhou's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction (2002) (914)
- Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning (2015) (313)
- 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 (2011) (302)
- Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor (2017) (278)
- Capturing non‐local interactions by long short‐term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility (2017) (272)
- A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. (2005) (263)
- Protein binding site prediction using an empirical scoring function (2006) (257)
- Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments (2004) (254)
- SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles (2012) (243)
- Interpreting the folding kinetics of helical proteins (1999) (238)
- Specific interactions for ab initio folding of protein terminal regions with secondary structures (2008) (237)
- Improving protein disorder prediction by deep bidirectional long short‐term memory recurrent neural networks (2016) (209)
- Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition (2004) (203)
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch? (2016) (195)
- The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers (2002) (182)
- A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding (2004) (182)
- Structural insights into the histone H1-nucleosome complex (2013) (176)
- Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions (1997) (172)
- SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method (2012) (162)
- Folding rate prediction using total contact distance. (2002) (161)
- An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state (2004) (158)
- RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning (2019) (152)
- Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells. (2019) (151)
- Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training (2006) (147)
- Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions (2008) (142)
- Community-wide assessment of protein-interface modeling suggests improvements to design methodology. (2011) (139)
- 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 (2009) (139)
- Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network (2014) (138)
- Quantifying the effect of burial of amino acid residues on protein stability (2003) (135)
- Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks (2018) (132)
- SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks. (2017) (131)
- Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks (2018) (126)
- Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. (2009) (120)
- Chemical association in simple models of molecular and ionic fluids (1989) (116)
- Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential (2004) (110)
- SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures (2005) (106)
- Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets (2010) (104)
- The calorimetric criterion for a two‐state process revisited (1999) (95)
- Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties (2007) (93)
- Fold recognition by concurrent use of solvent accessibility and residue depth (2007) (93)
- EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models. (2016) (91)
- Chemical association in simple models of molecular and ionic fluids. II. Thermodynamic properties (1992) (87)
- Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins (2016) (85)
- Chemical association in simple models of molecular and ionic fluids. III: The cavity function (1992) (84)
- Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function (2010) (82)
- BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences (2012) (80)
- Stability scale and atomic solvation parameters extracted from 1023 mutation experiments (2002) (79)
- SPARKS 2 and SP3 servers in CASP6 (2005) (79)
- Energy functions in de novo protein design: current challenges and future prospects. (2013) (78)
- Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden‐Markov‐model‐based method (2003) (78)
- SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning (2019) (75)
- Real‐value prediction of backbone torsion angles (2008) (74)
- A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction (2012) (73)
- SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008) (72)
- Single‐sequence‐based prediction of protein secondary structures and solvent accessibility by deep whole‐sequence learning (2018) (72)
- Fluids inside a pore—an integral-equation approach (1989) (72)
- Ion solvation dynamics in an interaction-site model solvent (1991) (71)
- DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile (2007) (67)
- DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels (2013) (66)
- Sequence‐based prediction of protein–peptide binding sites using support vector machine (2016) (66)
- EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments (2017) (60)
- SPIN2: Predicting sequence profiles from protein structures using deep neural networks (2018) (58)
- Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. (2019) (57)
- What is a desirable statistical energy functions for proteins and how can it be obtained? (2007) (56)
- Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures (2018) (56)
- Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction (2011) (56)
- Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation (2013) (55)
- A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys (2007) (52)
- Criticality of Charged Systems: I. the Restricted Primitive Model. (1995) (52)
- In-silico prediction of disorder content using hybrid sequence representation (2011) (51)
- Trends in template/fragment-free protein structure prediction (2010) (50)
- Structure‐based prediction of protein‐ peptide binding regions using Random Forest (2018) (50)
- Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. (2009) (50)
- DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels (2015) (49)
- Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. (2004) (48)
- Role of hydrophilic and hydrophobic contacts in folding of the second β‐hairpin fragment of protein G: Molecular dynamics simulation studies of an all‐atom model (2002) (47)
- Predicting residue–residue contact maps by a two‐layer, integrated neural‐network method (2009) (46)
- Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G. (2003) (46)
- Accurate single‐sequence prediction of solvent accessible surface area using local and global features (2014) (46)
- An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles (2009) (46)
- The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A (2002) (45)
- Small open reading frames: current prediction techniques and future prospect. (2011) (44)
- Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles (2014) (44)
- Systems-level understanding of ethanol-induced stresses and adaptation in E. coli (2017) (42)
- RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants (2019) (41)
- The dependence of all-atom statistical potentials on structural training database. (2004) (40)
- Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. (2016) (39)
- Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function (2005) (39)
- Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks (2008) (39)
- Consensus scoring for enriching near‐native structures from protein–protein docking decoys (2009) (39)
- Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. (2008) (39)
- Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes (2018) (37)
- Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome (2014) (37)
- Nucleotide Sugar Transporter SLC35 Family Structure and Function (2019) (35)
- Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions (2011) (35)
- DEPICTER: intrinsic disorder and disorder function prediction server. (2019) (35)
- FreeSASA : An open source C library for solvent accessible surface area calculations (2019) (34)
- Prediction of RNA binding proteins comes of age from low resolution to high resolution. (2013) (34)
- SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties (2019) (34)
- Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models (2015) (34)
- Phase separation of ionic fluids: an extended Ebeling-Grigo approach (1996) (34)
- Natural protein sequences are more intrinsically disordered than random sequences (2016) (34)
- Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers (2018) (34)
- Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water. (2003) (32)
- Nonlocal integral‐equation approximations. I. The zeroth order (hydrostatic) approximation with applications (1990) (32)
- 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 (2014) (31)
- A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions (2018) (31)
- Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening (2016) (31)
- Investigating DNA‐, RNA‐, and protein‐based features as a means to discriminate pathogenic synonymous variants (2017) (31)
- DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state (2019) (31)
- Analytical approach to molecular liquids. IV. Solvation dynamics and electron‐transfer reactions (1989) (30)
- Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. (2011) (30)
- Fluctuations of backbone torsion angles obtained from NMR‐determined structures and their prediction (2010) (30)
- Critical nucleation size in the folding of small apparently two‐state proteins (2004) (30)
- Thermodynamic perturbation theory for fused hard‐sphere and hard‐disk chain fluids (1995) (30)
- Thermodynamics and stability of a β‐sheet complex: Molecular dynamics simulations on simplified off‐lattice protein models (2004) (29)
- Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. (2014) (29)
- SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. (2014) (28)
- DescribePROT: database of amino acid-level protein structure and function predictions (2020) (28)
- Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks (2016) (27)
- Improving computational protein design by using structure‐derived sequence profile (2010) (27)
- The hard-sphere fluid: New exact results with applications (1988) (26)
- Structure-aware protein-protein interaction site prediction using deep graph convolutional network (2021) (26)
- Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning (2021) (26)
- Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B of Staphylococcal Protein A: Implication for the Origin of the Cooperativity of Protein Folding (2002) (26)
- Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning (2019) (25)
- Solute excluded‐volume effects on the stability of globular proteins: A statistical thermodynamic theory (1998) (24)
- Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease (2021) (24)
- Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction (2017) (24)
- Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model. (2007) (24)
- Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. (2006) (24)
- EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments (2020) (24)
- The dual role of a loop with low loop contact distance in folding and domain swapping (2002) (23)
- Note on standard free energy of transfer and partitioning of ionic species between two fluid phases (1988) (23)
- Carbohydrate‐binding protein identification by coupling structural similarity searching with binding affinity prediction (2014) (21)
- Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic (2016) (21)
- Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features (2018) (21)
- QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization (2006) (21)
- Folding thermodynamics of model four-strand antiparallel beta-sheet proteins. (2001) (21)
- The theory of semipermeable vesicles and membranes: An integral‐equation approach. I. General formalism and application to a hard‐sphere mixture (1988) (21)
- Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. (2008) (20)
- 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 (2005) (20)
- Improved fragment sampling for ab initio protein structure prediction using deep neural networks (2019) (20)
- Protein flexibility prediction by an all‐atom mean‐field statistical theory (2005) (20)
- Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome (2014) (20)
- Criticality of charged systems. II. The binary mixture of hard spheres and ions (1995) (20)
- SCUD: Fast structure clustering of decoys using reference state to remove overall rotation (2005) (19)
- SPOT‐ligand 2: improving structure‐based virtual screening by binding‐homology search on an expanded structural template library (2017) (19)
- Outer-sphere electron-transfer reactions in model molecular solvents : the mean spherical approximation (1991) (19)
- SPIN 2 : Predicting sequence profiles from protein structures using deep neural networks (2018) (18)
- Analytical approach to molecular liquids. I. Site–site interaction model using an extended mean‐spherical approximation (1989) (18)
- Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network (2020) (18)
- regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution (2017) (18)
- SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning (2021) (18)
- Fused hard‐sphere chain molecules: Comparison between Monte Carlo simulation for the bulk pressure and generalized Flory theories (1995) (18)
- Fluids inside a pore—an integral-equation approach: II. Cylindrical pores (1989) (17)
- Critical assessment of protein intrinsic disorder prediction (2021) (17)
- sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections (2016) (17)
- Equations of state for hard-sphere fluids (1988) (17)
- RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis (2021) (17)
- Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning (2020) (17)
- DNA sequence repeats identify numerous Type I restriction‐modification systems that are potential epigenetic regulators controlling phase‐variable regulons; phasevarions (2019) (17)
- Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement (2021) (16)
- The theory of semipermeable vesicles and membranes: An integral‐equation approach. II. Donnan equilibrium (1988) (16)
- Linear dependence on chain length for the thermodynamic properties of tangent hard-sphere chains (1995) (16)
- Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge (2019) (15)
- From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs (2021) (15)
- Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures (2018) (15)
- Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs. (2002) (15)
- SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity (2016) (15)
- Prediction of One‐Dimensional Structural Properties Of Proteins by Integrated Neural Networks (2010) (15)
- The helix–coil transition revisited (2007) (14)
- Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning (2018) (14)
- Nonlocal integral‐equation approximations. II. Lennard‐Jones fluids (1990) (14)
- Analytical approach to molecular liquids. II. Solvation of ions in molecular fluids (1989) (14)
- Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines (2016) (14)
- SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites (2019) (14)
- Microscopic modelling of association (1992) (13)
- Assessment of methods for predicting the effects of PTEN and TPMT protein variants (2019) (13)
- Analytical approach to molecular liquids. V. Symmetric dissociative dipolar dumbbells with the bonding length σ/3≤L≤σ/2 and related systems (1993) (13)
- Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10 (2016) (13)
- Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination (2020) (13)
- Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA (2017) (13)
- ExonImpact: Prioritizing Pathogenic Alternative Splicing Events (2017) (12)
- Refining near‐native protein–protein docking decoys by local resampling and energy minimization (2009) (12)
- Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite (2016) (12)
- Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function (2005) (12)
- Analytical approach to molecular liquids. III. The Born solvation free energy of two fixed ions in a dipolar solvent (1989) (12)
- DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins (2017) (11)
- B‐factor profile prediction for RNA flexibility using support vector machines (2018) (11)
- Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity (2019) (11)
- Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids (2018) (11)
- All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State (2020) (11)
- Prediction of Protein Secondary Structure (2017) (11)
- Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI (2017) (10)
- Intrinsic Disorder and Semi-disorder Prediction by SPINE-D. (2016) (10)
- LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction (2016) (10)
- Domain graph of Arabidopsis proteome by comparative analysis. (2005) (9)
- Exact results for isolated sticky chains (1995) (9)
- Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment (2021) (9)
- RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks (2021) (9)
- Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling (2022) (9)
- CHEMICAL ASSOCIATION IN SIMPLE MODELS OF MOLECULAR AND IONIC FLUIDS. IV: NEW APPROXIMATION FOR THE CAVITY FUNCTION AND AN APPLICATION TO THE THEORY OF WEAK ELECTROLYTES (1995) (9)
- SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model (2022) (9)
- Argonaute proteins: structures and their endonuclease activity (2021) (9)
- Fluids inside a pore: an integral equation approach. III: Water-in-oil microemulsions (1989) (9)
- SPOT‐Fold: Fragment‐Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map (2019) (8)
- Folding Thermodynamics of Model Four-Strand Antiparallel -Sheet Proteins (2002) (7)
- Salt Effects on Protein Titration and Binding (1998) (7)
- Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations. (2020) (6)
- Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile. (2017) (6)
- Predicting functional long non-coding RNAs validated by low throughput experiments (2019) (6)
- Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations. (2019) (6)
- Electron rearrangement and energy relaxation due to a core hole creation in molecules (1992) (5)
- A heuristic for the time constrained asymmetric linear sum assignment problem (2017) (5)
- The role of semidisorder in temperature adaptation of bacterial FlgM proteins. (2013) (5)
- Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana (2012) (5)
- YesU from Bacillus subtilis preferentially binds fucosylated glycans (2018) (5)
- Experimentally Validated Plant lncRNAs in EVLncRNAs Database. (2019) (5)
- Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease (2020) (5)
- Machine learning models in protein bioinformatics. (2011) (5)
- Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016 (2019) (5)
- Self‐derived structure‐disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides (2018) (4)
- Design and folding of a multidomain protein. (2005) (4)
- Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes. (2006) (4)
- Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers (1996) (4)
- Discriminating between disease-causing and neutral non-frameshifting micro-INDELs by support vector machines by means of integrated sequence- and structure-based features (2013) (4)
- De novo protein design by an energy function based on series expansion in distance and orientation dependence (2021) (3)
- Effective protein conformational sampling based on predicted torsion angles (2016) (3)
- Performance of in silico tools for the evaluation of p 16 INK 4 a ( CDKN 2 A ) variants in CAGI (2017) (3)
- Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites (2018) (3)
- Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water (2006) (2)
- SPOT-Contact-Single: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model (2021) (2)
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives (2022) (2)
- The theory of semipermeable vesicles and membranes: An integral‐equation approach. III. Vesicles with internal nonpermeating ions (1989) (2)
- Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation (2013) (2)
- Recipe for a Quality Scientific Paper: Fulfill Readers! and Reviewers! Expectations (2007) (2)
- GM-DockZn: a geometry matching-based docking algorithm for zinc proteins (2020) (2)
- Improved RNA homology detection and alignment by automatic iterative search in an expanded database (2022) (2)
- RegSNPs-Intron: A computational framework for prioritizing Intronic Single Nucleotide Variants in Human Genetic Disease (2019) (1)
- Erratum: Structural insights into the histone H1-nucleosome complex (Proceedings of the National Academy of Sciences of the United States of America (2013) 110:48 (19390-19395) DOI: 10.1073/pnas.1314905110) (2014) (1)
- Investigation of weak damage in Al0.25Ga0.75As/GaAs by using RBS/C and Raman spectroscopy (2001) (1)
- Fast and accurate thermodynamics of square-well systems from umbrella- sampling simulations of hard-sphere systems (2001) (1)
- DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels (2013) (1)
- RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis (2020) (1)
- High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5′-OH-end linker and unique 3′-P-end fragments from hydroxyl radical cleavage (2022) (1)
- Charting the Unexplored RNA-binding Protein Atlas of the Human Genome (2000) (1)
- DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks (2021) (1)
- From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design (2010) (0)
- Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination (2020) (0)
- SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks (2021) (0)
- Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures (2018) (0)
- Zhou domain – domain interaction profile DDOMAIN : Dividing structures into domains using a normalized (0)
- Chapter 10 Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profi le (2016) (0)
- ( N – 1 ) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment (2005) (0)
- DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins (2017) (0)
- Accessible surface area of proteins from purely sequence information and the importance of global features (2014) (0)
- Protein Structure Prediction (2009) (0)
- Computational Prediction of N- and O-Linked Glycosylation Sites for Human and Mouse Proteins. (2022) (0)
- Resurrecting self-cleaving mini-ribozymes from 40-million-year-old LINE-1 elements in human genome (2021) (0)
- The classification of the web servers available on (2011) (0)
- Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential. (2021) (0)
- ) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment N Sequences (2005) (0)
- Self-Inhibitory Peptides Targeting the Neisseria gonorrhoeae MtrCDE Efflux Pump Increase Antibiotic Susceptibility (2021) (0)
- General Formalisms and Hard Spheres inside Spherical and Slit Pores (1967) (0)
- Natural protein sequences are more intrinsically disordered than random sequences (2016) (0)
- Toward a physical energy function for intra- and inter-protein interactions by combining structural knowledge with physical principles (2004) (0)
- High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. (2022) (0)
- NONLOCAL INTEGRAL-EQUATION APPROXIMATIONS : n (2005) (0)
- Replication Data for: Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA (2017) (0)
- Unbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential (2004) (0)
- Chemical assoc. in simple models of molecular ionic fluids II (1991) (0)
- Structural bioinformatics LRFragLib : an effective algorithm to identify fragments for de novo protein structure prediction (2017) (0)
- Issue Information (2017) (0)
- Chapter 6 SPIDER 2 : A Package to Predict Secondary Structure , Accessible Surface Area , and Main-Chain Torsional Angles by Deep Neural Networks (2016) (0)
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What Schools Are Affiliated With Yaoqi Zhou?
Yaoqi Zhou is affiliated with the following schools:
