All Stories

  1. Predicting functional long non-coding RNAs validated by low throughput experiments
  2. Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations
  3. Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides
  4. EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments
  5. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants
  6. Faculty of 1000 evaluation for Widespread position-specific conservation of synonymous rare codons within coding sequences.
  7. Faculty of 1000 evaluation for A high-throughput approach to profile RNA structure.
  8. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI
  9. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution
  10. DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins
  11. Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor
  12. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
  13. SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library
  14. Prediction of Protein Secondary Structure
  15. Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
  16. Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks
  17. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction
  18. SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks
  19. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile
  20. Intrinsic Disorder and Semi-disorder Prediction by SPINE-D
  21. Sequence-Based Prediction of Protein–Carbohydrate Binding Sites Using Support Vector Machines
  22. LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction
  23. ExonImpact: Prioritizing Pathogenic Alternative Splicing Events
  24. Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks
  25. Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite
  26. Faculty of 1000 evaluation for Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.
  27. Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening
  28. Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10
  29. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity
  30. EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models
  31. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections
  32. Sequence-based prediction of protein-peptide binding sites using support vector machine
  33. Natural protein sequences are more intrinsically disordered than random sequences
  34. Effective protein conformational sampling based on predicted torsion angles
  35. A heuristic for the time constrained asymmetric linear sum assignment problem
  36. Faculty of 1000 evaluation for Designed protein reveals structural determinants of extreme kinetic stability.
  37. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins
  38. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic
  39. Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models
  40. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning
  41. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels
  42. Accurate single-sequence prediction of solvent accessible surface area using local and global features
  43. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction
  44. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network
  45. Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles
  46. Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome
  47. Faculty Opinions recommendation of An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.
  48. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation
  49. SPOT-Seq-RNA: Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction
  50. Correction for Zhou et al., Structural insights into the histone H1-nucleosome complex
  51. 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
  52. The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins
  53. Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome
  54. Structural insights into the histone H1-nucleosome complex
  55. Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation
  56. Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects
  57. Prediction of RNA binding proteins comes of age from low resolution to high resolution
  58. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels
  59. BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences
  60. A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction
  61. Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana
  62. SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method
  63. SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
  64. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction
  65. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
  66. Editorial [Hot Topic: Machine Learning Models in Protein Bioinformatics (Guest Editors: Lukasz Kurgan & Yaoqi Zhou)]
  67. Small Open Reading Frames: Current Prediction Techniques and Future Prospect
  68. In-silico prediction of disorder content using hybrid sequence representation
  69. 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
  70. A data processing software package for passive seismic monitoring of hydraulic fracturing
  71. Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations
  72. Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions
  73. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
  74. Fluctuations of backbone torsion angles obtained from NMR‐determined structures and their prediction
  75. Prediction of One‐Dimensional Structural Properties Of Proteins by Integrated Neural Networks
  76. Trends in template/fragment-free protein structure prediction
  77. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
  78. Improving computational protein design by using structure‐derived sequence profile
  79. Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction
  80. An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles
  81. Refining near‐native protein–protein docking decoys by local resampling and energy minimization
  82. Predicting residue–residue contact maps by a two‐layer, integrated neural‐network method
  83. Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations
  84. Consensus scoring for enriching near‐native structures from protein–protein docking decoys
  85. 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
  86. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions
  87. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
  88. Folding mechanisms of individual β-hairpins in a Gō model of Pin1 WW domain by all-atom molecular dynamics simulations
  89. SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model
  90. Specific interactions for ab initio folding of protein terminal regions with secondary structures
  91. Real‐value prediction of backbone torsion angles
  92. Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks
  93. Temperature-Dependent Folding Pathways of Pin1 WW Domain: An All-Atom Molecular Dynamics Simulation of a Gō Model
  94. A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
  95. The helix–coil transition revisited
  96. Fold recognition by concurrent use of solvent accessibility and residue depth
  97. DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile
  98. Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties
  99. Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training
  100. Perineural clonidine reduces p38 mitogen-activated protein kinase activation in sensory neurons
  101. Protein binding site prediction using an empirical scoring function
  102. Fast and Accurate Method for Identifying High-Quality Protein-Interaction Modules by Clique Merging and Its Application to Yeast
  103. QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization
  104. Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water
  105. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes
  106. What is a Desirable Statistical Energy Function for Proteins and How Can It Be Obtained?
  107. Relevance judgment: What do information users consider beyond topicality?
  108. FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION
  109. Design and Folding of a Multidomain Protein
  110. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
  111. Protein flexibility prediction by an all‐atom mean‐field statistical theory
  112. 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
  113. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
  114. SCUD: Fast structure clustering of decoys using reference state to remove overall rotation
  115. A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
  116. Domain Graph of Arabidopsis Proteome by Comparative Analysis
  117. SPARKS 2 and SP3 servers in CASP6
  118. Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments
  119. The Dependence of All-Atom Statistical Potentials on Structural Training Database
  120. Critical nucleation size in the folding of small apparently two‐state proteins
  121. A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
  122. Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition
  123. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
  124. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
  125. Assembly and Kinetic Folding Pathways of a Tetrameric β-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models
  126. Thermodynamics and stability of a  -sheet complex: Molecular dynamics simulations on simplified off-lattice protein models
  127. Quantifying the effect of burial of amino acid residues on protein stability
  128. CORRECTION
  129. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden‐Markov‐model‐based method
  130. Temperature Dependence of the Distribution of the First Passage Time:  Results from Discontinuous Molecular Dynamics Simulations of an All-Atom Model of the Second β-Hairpin Fragment of Protein G
  131. Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and Elucidation of the Role of Interfacial Water
  132. 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
  133. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
  134. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
  135. Protein Folding Pathways and Kinetics: Molecular Dynamics Simulations of β-Strand Motifs
  136. The dual role of a loop with low loop contact distance in folding and domain swapping
  137. 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
  138. Folding Thermodynamics of Model Four-Strand Antiparallel β-Sheet Proteins
  139. The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers
  140. Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B ofStaphylococcalProtein A:  Implication for the Origin of the Cooperativity of Protein Folding
  141. Folding Rate Prediction Using Total Contact Distance
  142. Fast and accurate thermodynamics of square-well systems from umbrella-sampling simulations of hard-sphere systems
  143. Protein Motions at Zero-Total Angular Momentum: The Importance of Long-Range Correlations
  144. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis 1 1Edited by A. R. Fersht
  145. Interpreting the folding kinetics of helical proteins
  146. The calorimetric criterion for a two‐state process revisited
  147. Native proteins are surface-molten solids: application of the lindemann criterion for the solid versus liquid state
  148. Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory
  149. Salt Effects on Protein Titration and Binding
  150. Folding thermodynamics of a model three-helix-bundle protein
  151. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
  152. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers
  153. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers
  154. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model
  155. Solute excluded‐volume effects on the stability of globular proteins: A statistical thermodynamic theory
  156. Phase Separation of Ionic Fluids:  An Extended Ebeling−Grigo Approach
  157. Exact results for isolated sticky chains
  158. Linear dependence on chain length for the thermodynamic properties of tangent hard-sphere chains
  159. Thermodynamic perturbation theory for fused hard-sphere and hard-disk chain fluids
  160. 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
  161. Fused hard-sphere chain molecules: Comparison between Monte Carlo simulation for the bulk pressure and generalized Flory theories
  162. Criticality of charged systems. I. The restricted primitive model
  163. Criticality of charged systems. II. The binary mixture of hard spheres and ions
  164. Analytical approach to molecular liquids. V. Symmetric dissociative dipolar dumbbells with the bonding length σ/3≤L≤σ/2 and related systems
  165. Microscopic modelling of association
  166. Electron rearrangement and energy relaxation due to a core hole creation in molecules
  167. Chemical association in simple models of molecular and ionic fluids. III. The cavity function
  168. Chemical association in simple models of molecular and ionic fluids. II. Thermodynamic properties
  169. Outer-sphere electron-transfer reactions in model molecular solvents: the mean spherical approximation
  170. Ion solvation dynamics in an interaction-site model solvent
  171. Nonlocal integral-equation approximations. II. Lennard-Jones fluids
  172. Nonlocal integral-equation approximations. I. The zeroth order (hydrostatic) approximation with applications
  173. Fluids inside a pore—An integral equation approach
  174. Analytical approach to molecular liquids. II. Solvation of ions in molecular fluids
  175. Analytical approach to molecular liquids. I. Site–site interaction model using an extended mean-spherical approximation
  176. Analytical approach to molecular liquids. III. The Born solvation free energy of two fixed ions in a dipolar solvent
  177. Analytical approach to molecular liquids. IV. Solvation dynamics and electron-transfer reactions
  178. Chemical association in simple models of molecular and ionic fluids
  179. The theory of semipermeable vesicles and membranes: An integral-equation approach. III. Vesicles with internal nonpermeating ions
  180. Fluids inside a pore—an integral-equation approach
  181. Fluids inside a pore—an integral-equation approach
  182. The theory of semipermeable vesicles and membranes: An integral-equation approach. II. Donnan equilibrium
  183. The theory of semipermeable vesicles and membranes: An integral-equation approach. I. General formalism and application to a hard-sphere mixture
  184. Equations of state for hard-sphere fluids
  185. Note on standard free energy of transfer and partitioning of ionic species between two fluid phases
  186. The hard-sphere fluid: New exact results with applications
  187. Faculty of 1000 evaluation for Evaluating template-based and template-free protein-protein complex structure prediction.
  188. Faculty of 1000 evaluation for Golden triangle for folding rates of globular proteins.
  189. Faculty of 1000 evaluation for Evolutionary optimization of protein folding.
  190. Faculty of 1000 evaluation for Buried and accessible surface area control intrinsic protein flexibility.
  191. Faculty of 1000 evaluation for Residue level quantification of protein stability in living cells.
  192. Faculty of 1000 evaluation for Quantitative modeling of transcription factor binding specificities using DNA shape.
  193. Faculty of 1000 evaluation for Single-molecule correlated chemical probing of RNA.
  194. Faculty of 1000 evaluation for Removing T-cell epitopes with computational protein design.
  195. Faculty of 1000 evaluation for Knowledge discovery by accuracy maximization.
  196. Faculty of 1000 evaluation for Specific RNA-Binding Antibodies with a Four-Amino-Acid Code.
  197. Faculty of 1000 evaluation for Protein-protein association rates captured in a single geometric parameter.
  198. Faculty of 1000 evaluation for Inactive conformation enhances binding function in physiological conditions.
  199. Faculty of 1000 evaluation for Blind prediction of charged ligand binding affinities in a model binding site.
  200. Faculty of 1000 evaluation for Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface.
  201. Faculty of 1000 evaluation for The s2D Method: Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins.
  202. Faculty of 1000 evaluation for The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease.
  203. Protein Structure Prediction