Proteins-Structure Function and Bioinformatics

Article	Citations
Critical assessment of methods of protein structure prediction (CASP)—Round XIV	270
Applying and improving AlphaFold at CASP14	216
High‐accuracy protein structure prediction in CASP14	207
Human SARS CoV‐2 spike protein mutations	141
Multi‐state modeling of G‐protein coupled receptors at experimental accuracy	79
Perturbing the energy landscape for improved packing during computational protein design	76
Plastics degradation by hydrolytic enzymes: The plastics‐active enzymes database—PAZy	75
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	67
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges	47
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	45
Assessing the utility of CASP14 models for molecular replacement	41
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods	36
Energy‐based graph convolutional networks for scoring protein docking models	36
Assessment of the CASP14 assembly predictions	35
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14	35
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination	33
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	32
Assessment of thePETaseconformational changes induced by poly(ethylene terephthalate) binding	31
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)	31
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes	31
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2	29
When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14—(tFold for CASP14 contact prediction)	27
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP	27
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	27
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease	26

Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	26
Evolutionary relationships and sequence‐structure determinants in human SARS coronavirus‐2 spike proteins for host receptor recognition	25
Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases	25
Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?	25
Target highlights in CASP14: Analysis of models by structure providers	24
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures	24
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning	23
Multicopper oxidases: modular structure, sequence space, and evolutionary relationships	22
Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment	21
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction	21
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic	20
Why are ACE2 binding coronavirus strains SARS‐CoV/SARS‐CoV‐2 wild and NL63 mild?	20
ACE2‐based decoy receptors for SARS coronavirus 2	20
Evaluation of model refinement in CASP14	19
Application of docking methodologies to modeled proteins	19
Using machine learning to improve ensemble docking for drug discovery	18
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐2	18
Recent progress in the structural biology of P2X receptors	18
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	18
Physics‐based protein structure refinement in the era of artificial intelligence	17
Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations	17
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14	17
Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer	16
Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism	16
Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome	16
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability	16
Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism	16
New prediction categories in CASP15	16
Protein oligomer modeling guided by predicted interchain contacts in CASP14	15
Molecular dynamics simulations identify the regions of compromised thermostability in SazCA	15
Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting	15
Predicting protein flexibility with AlphaFold	15
Assessing the accuracy of contact and distance predictions in CASP14	14
New amino acid substitution matrix brings sequence alignments into agreement with structure matches	14
SidechainNet: An all‐atom protein structure dataset for machine learning	14
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	14
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	14
Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies	13
High‐resolution structure of a partially folded insulin aggregation intermediate	13
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling	13
Identification of biochemically neutral positions in liver pyruvate kinase	13
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15	13
PDB‐tools web: A user‐friendly interface for the manipulation of PDB files	13
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	13
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	13
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	13
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction	12
Tertiary structure assessment at CASP15	12
A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains	12
A protein sequence fitness function for identifying natural and nonnatural proteins	12

Biological nanopores for sensing applications	12
The actin cytoskeleton orchestra in Entamoeba histolytica	12
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	11
From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation	11
Comparative protein structure network analysis on 3CLpro from SARS‐CoV‐1 and SARS‐CoV‐2	11
Using normal mode analysis on protein structural models. How far can we go on our predictions?	11
Cryo‐EM targets in CASP14	10
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma	10
Assessing the binding properties of CASP14 targets and models	10
Insights into the mechanisms of light‐oxygen‐voltage domain color tuning from a set of high‐resolution X‐ray structures	10
Analyses of protein cores reveal fundamental differences between solution and crystal structures	10
Assessment of three‐dimensional RNA structure prediction in CASP15	10
Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH	10
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots	10
Genome‐wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights	10
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments	9
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	9
Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution	9
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	9
Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB	9
Improved multimer prediction using massive sampling with AlphaFold in CASP15	9
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses	9
RNA target highlights in CASP15: Evaluation of predicted models by structure providers	9
Exploring the structure and dynamics of proteins in soil organic matter	9
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses	9
Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation	9
Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker	9
Structural compliance: A new metric for protein flexibility	8
Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes	8
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	8
Critical assessment of methods of protein structure prediction (CASP)—Round XV	8
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)	8
Expansin Engineering Database: A navigation and classification tool for expansins and homologues	8
Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding	8
The effect of lipid composition on the dynamics of tau fibrils	8
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors	8
Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures	8
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	8
A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats	8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	7
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics study	7
Estimation of model accuracy in CASP15 using the ModFOLDdock server	7
Protein structure search to support the development of protein structure prediction methods	7
A rod conformation of the Pyrococcus furiosus Rad50 coiled coil	7
Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model	7
Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3‐5 EMBL‐EBI, Hinxton, UK	7
Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin	7
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	7
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	7
Isolation and characterization of ACE‐I inhibitory peptides from ribbonfish for a potential inhibitor of the main protease of SARS‐CoV‐2: An in silico analysis	7
Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 2	7
Ca2+ as cofactor of the mitochondrial H+‐translocating F1FO‐ATP(hydrol)ase	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
A detailed mapping of the readily accessible disulphide bonds in the cortex of wool fibres	6
Proteome analysis of the circadian clock protein PERIOD2	6
Are granulins copper sequestering proteins?	6
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues	6
Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis	6
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15	6
The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors	6
Calcium inhibits penetration of Alzheimer's Aβ1–42 monomers into the membrane	6
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	6
Performance of human and server prediction in CAPRI rounds 38‐45	6
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	6
Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean	6
Conserved internal hydration motifs in protein kinases	6
Structural studies on 10‐hydroxygeraniol dehydrogenase: A novel linear substrate‐specific dehydrogenase from Catharanthus roseus	6
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study	6
Protein target highlights in CASP15: Analysis of models by structure providers	6
ANOVA‐particle swarm optimization‐based feature selection and gradient boosting machine classifier for improved protein–protein interaction prediction	6
Predicting mutant outcome by combining deep mutational scanning and machine learning	6
Mapping of antibody epitopes based on docking and homology modeling	6
A computer aided drug discovery based discovery of lead‐like compounds against KDM5A for cancers using pharmacophore modeling and high‐throughput virtual screening	6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	6
RNA tertiary structure modeling with BRiQ potential in CASP15	6
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	6
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	6
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	6

A geometrical framework for thinking about proteins	6
Template‐based modeling and ab‐initio docking using CoDock in CAPRI	6
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	6
Circuit topology predicts pathogenicity of missense mutations	6
Assessment of protein–ligand complexes in CASP15	6
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	6
Study on functional sites in human multidrug resistance protein 1 (hMRP1)	5
Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor	5
Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis	5
Dihydrolipoamide dehydrogenase moonlighting activity as a DNA chelating agent	5
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	5
The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils	5
Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods	5
Consistency and variation of protein subcellular location annotations	5
Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers?	5
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors	5
Conformational changes in a Vernier zone region: Implications for antibody dual specificity	5
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks	5
Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B	5
PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints	5
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking	5
Tuning the binding interface between Machupo virus glycoprotein and human transferrin receptor	5
Inhibition of Mycobacterium tuberculosisInhA by 3‐nitropropanoic acid	5
Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide	5
Novel antimicrobial anionic cecropins from the spruce budworm feature a poly‐L‐aspartic acid C‐terminus	5
Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation	5
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
RF‐SVM: Identification of DNA‐binding proteins based on comprehensive feature representation methods and support vector machine	5
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	5
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	5
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	5
Protein dynamics analysis identifies candidate cancer driver genes and mutations in TCGA data	5
Enhancing the promiscuity of a member of the Caspase protease family by rational design	5
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium	5
From propensities to patterns to principles in protein folding	5
Simplified geometric representations of protein structures identify complementary interaction interfaces	5
Distinctive communication networks in inactive states of β2‐adrenergic receptor: Mutual information and entropy transfer analysis	5
Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior	4
Common mechanism of thermostability in small α‐ and β‐proteins studied by molecular dynamics	4
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15	4
Crystal structure of a S‐adenosyl‐L‐methionine‐dependent O‐methyltransferase‐like enzyme from Aspergillus flavus	4
Assessment of the assessment—All about complexes	4
II. Geometrical framework for thinking about globular proteins: The power of poking	4
Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 α‐receptor	4
Protein oligomer structure prediction using GALAXY in CASP14	4
Total free energy analysis of fully hydrated proteins	4
Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation	4
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	4
A Maximum Caliber analysis of the Foldon Hypothesis	4
The X‐ray crystal structure of human A15C neuroglobin reveals both native/de novo disulfide bonds and unexpected ligand‐binding sites	4
Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase	4
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane	4
Sequence and evolutionary analysis of bacterial ribosomal S1 proteins	4
Dockground scoring benchmarks for protein docking	4
Remarked suppression of Aβ42 protomer–protomer dissociation reaction elucidated by molecular dynamics simulation	4
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	4
New tyrosinases with putative action against contaminants of emerging concern	4
Structures and interactions of insulin‐like peptides from cone snail venom	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Substrate‐assisted activation and selectivity of the bacterial RavD effector deubiquitinylase	4
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	4
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	4
Inferring metal binding sites in flexible regions of proteins	4
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	4
Introduction of a new scheme for classifying β‐turns in protein structures	4
Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target	4
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks	4
Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites	4
Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis	4
Further thermo‐stabilization of thermophilic rhodopsin from Thermus thermophilusJL‐18 through engineering in extramembrane regions	4
Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites	4
RNA tertiary structure prediction using RNAComposer in CASP15	4
MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH	4
A new method for protein characterization and classification using geometrical features for 3D face analysis: An example of tubulin structures	4
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	4
Influence of electrostatic forces on the association kinetics and conformational ensemble of an intrinsically disordered protein	4
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	4
Insights into modular polyketide synthase loops aided by repetitive sequences	4
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	4
Crystal‐structures‐guided design of fragment‐based drugs for inhibiting the main protease of SARS‐CoV‐2	4
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	4
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	4
Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single‐particle cryo‐EM	4
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase	4
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15	4
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	4
The protonation state of Glu202 in acetylcholinesterase	4
β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils	4
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	4
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	3
Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies	3
Scoring of protein–protein docking models utilizing predicted interface residues	3
RosettaCM for antibodies with very long HCDR3s and low template availability	3
Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank	3