Proteins-Structure Function and Bioinformatics

Article	Citations
Critical assessment of methods of protein structure prediction (CASP)—Round XIV	293
Applying and improving AlphaFold at CASP14	233
High‐accuracy protein structure prediction in CASP14	223
Human SARS CoV‐2 spike protein mutations	143
Plastics degradation by hydrolytic enzymes: The plastics‐active enzymes database—PAZy	86
Multi‐state modeling of G‐protein coupled receptors at experimental accuracy	86
Perturbing the energy landscape for improved packing during computational protein design	85
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	72
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges	48
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	47
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods	42
Assessing the utility of CASP14 models for molecular replacement	41
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14	38
Assessment of the CASP14 assembly predictions	36
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination	35
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	33
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)	33
Assessment of thePETaseconformational changes induced by poly(ethylene terephthalate) binding	32
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes	32
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	30
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2	29
Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	28
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures	28
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease	28
Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?	28

AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP	27
When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14—(tFold for CASP14 contact prediction)	27
Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases	26
Evolutionary relationships and sequence‐structure determinants in human SARS coronavirus‐2 spike proteins for host receptor recognition	26
Target highlights in CASP14: Analysis of models by structure providers	25
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic	25
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning	24
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction	23
Why are ACE2 binding coronavirus strains SARS‐CoV/SARS‐CoV‐2 wild and NL63 mild?	22
New prediction categories in CASP15	22
Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment	22
Recent progress in the structural biology of P2X receptors	22
Multicopper oxidases: modular structure, sequence space, and evolutionary relationships	22
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	20
ACE2‐based decoy receptors for SARS coronavirus 2	20
Evaluation of model refinement in CASP14	19
Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome	19
Using machine learning to improve ensemble docking for drug discovery	19
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐2	19
Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations	18
Physics‐based protein structure refinement in the era of artificial intelligence	18
Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer	18
Predicting protein flexibility with AlphaFold	18
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14	18
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	18
A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains	17
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability	17
Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism	17
Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting	16
Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism	16
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15	15
Assessing the accuracy of contact and distance predictions in CASP14	15
Assessment of three‐dimensional RNA structure prediction in CASP15	15
Protein oligomer modeling guided by predicted interchain contacts in CASP14	15
Molecular dynamics simulations identify the regions of compromised thermostability in SazCA	15
Critical assessment of methods of protein structure prediction (CASP)—Round XV	14
Biological nanopores for sensing applications	14
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	14
SidechainNet: An all‐atom protein structure dataset for machine learning	14
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	14
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction	14
Tertiary structure assessment at CASP15	14
New amino acid substitution matrix brings sequence alignments into agreement with structure matches	14
Comparative protein structure network analysis on 3CLpro from SARS‐CoV‐1 and SARS‐CoV‐2	13
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	13
Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies	13
A protein sequence fitness function for identifying natural and nonnatural proteins	13
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling	13
The actin cytoskeleton orchestra in Entamoeba histolytica	13
Identification of biochemically neutral positions in liver pyruvate kinase	13

High‐resolution structure of a partially folded insulin aggregation intermediate	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
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma	12
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	12
From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation	12
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	12
Exploring the structure and dynamics of proteins in soil organic matter	11
Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker	11
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments	11
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots	11
Genome‐wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights	11
Using normal mode analysis on protein structural models. How far can we go on our predictions?	11
RNA target highlights in CASP15: Evaluation of predicted models by structure providers	11
Insights into the mechanisms of light‐oxygen‐voltage domain color tuning from a set of high‐resolution X‐ray structures	11
Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH	10
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	10
Cryo‐EM targets in CASP14	10
Assessing the binding properties of CASP14 targets and models	10
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses	10
Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB	9
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	9
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses	9
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	9
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)	9
Expansin Engineering Database: A navigation and classification tool for expansins and homologues	9
Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation	9
Estimation of model accuracy in CASP15 using the ModFOLDdock server	9
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	9
Improved multimer prediction using massive sampling with AlphaFold in CASP15	9
Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 2	9
Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution	9
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	9
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors	8
Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes	8
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	8
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	8
The effect of lipid composition on the dynamics of tau fibrils	8
Structural compliance: A new metric for protein flexibility	8
Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures	8
Assessment of protein–ligand complexes in CASP15	8
Plastic structures for diverse substrates: A revisit of human ABC transporters	8
From propensities to patterns to principles in protein folding	8
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15	8
Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding	8
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	8
Protein target highlights in CASP15: Analysis of models by structure providers	8
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	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
Mapping of antibody epitopes based on docking and homology modeling	7
Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin	7
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	7
Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model	7
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics study	7
RNA tertiary structure modeling with BRiQ potential in CASP15	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
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	7
Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis	7
Ca2+ as cofactor of the mitochondrial H+‐translocating F1FO‐ATP(hydrol)ase	7
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	6
Performance of human and server prediction in CAPRI rounds 38‐45	6
Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean	6
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study	6
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	6
A geometrical framework for thinking about proteins	6
Assessment of the assessment—All about complexes	6
The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors	6
RF‐SVM: Identification of DNA‐binding proteins based on comprehensive feature representation methods and support vector machine	6
Circuit topology predicts pathogenicity of missense mutations	6
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	6
Conserved internal hydration motifs in protein kinases	6
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues	6
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	6
Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis	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
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	6

Proteome analysis of the circadian clock protein PERIOD2	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
A detailed mapping of the readily accessible disulphide bonds in the cortex of wool fibres	6
Are granulins copper sequestering proteins?	6
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	6
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	6
The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils	6
Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor	6
Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites	6
Calcium inhibits penetration of Alzheimer's Aβ1–42 monomers into the membrane	6
Further thermo‐stabilization of thermophilic rhodopsin from Thermus thermophilusJL‐18 through engineering in extramembrane regions	5
Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods	5
Tuning the binding interface between Machupo virus glycoprotein and human transferrin receptor	5
Novel antimicrobial anionic cecropins from the spruce budworm feature a poly‐L‐aspartic acid C‐terminus	5
Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B	5
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	5
Dihydrolipoamide dehydrogenase moonlighting activity as a DNA chelating agent	5
Conformational changes in a Vernier zone region: Implications for antibody dual specificity	5
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	5
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors	5
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
RNA tertiary structure prediction using RNAComposer in CASP15	5
Inhibition of Mycobacterium tuberculosisInhA by 3‐nitropropanoic acid	5
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium	5
Consistency and variation of protein subcellular location annotations	5
Sequence and evolutionary analysis of bacterial ribosomal S1 proteins	5
Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation	5
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	5
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	5
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints	5
Study on functional sites in human multidrug resistance protein 1 (hMRP1)	5
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase	5
Structures and interactions of insulin‐like peptides from cone snail venom	5
Enhancing the promiscuity of a member of the Caspase protease family by rational design	5
Protein dynamics analysis identifies candidate cancer driver genes and mutations in TCGA data	5
Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide	5
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane	5
Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers?	5
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	5
Distinctive communication networks in inactive states of β2‐adrenergic receptor: Mutual information and entropy transfer analysis	5
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	5
Simplified geometric representations of protein structures identify complementary interaction interfaces	5
Inferring metal binding sites in flexible regions of proteins	5
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks	5
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	5
The X‐ray crystal structure of human A15C neuroglobin reveals both native/de novo disulfide bonds and unexpected ligand‐binding sites	4
Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target	4
Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis	4
Structural insights at acidic pH of dye‐decolorizing peroxidase from Bacillus subtilis	4
Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase	4
Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior	4
II. Geometrical framework for thinking about globular proteins: The power of poking	4
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15	4
New tyrosinases with putative action against contaminants of emerging concern	4
Substrate‐assisted activation and selectivity of the bacterial RavD effector deubiquitinylase	4
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	4
Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 α‐receptor	4
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	4
Crystal‐structures‐guided design of fragment‐based drugs for inhibiting the main protease of SARS‐CoV‐2	4
Total free energy analysis of fully hydrated proteins	4
Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single‐particle cryo‐EM	4
Structural and functional analysis of the human cone‐rod homeobox transcription factor	4
Identification of key molecular players and associated pathways in cervical squamous cell carcinoma progression through network analysis	4
A monomeric structure of human TMEM63A protein	4
MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH	4
The protonation state of Glu202 in acetylcholinesterase	4
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Influence of electrostatic forces on the association kinetics and conformational ensemble of an intrinsically disordered protein	4
Crystal structure of a S‐adenosyl‐L‐methionine‐dependent O‐methyltransferase‐like enzyme from Aspergillus flavus	4
Insights into modular polyketide synthase loops aided by repetitive sequences	4
Scoring of protein–protein docking models utilizing predicted interface residues	4
Evidence for the preferential reuse of sub‐domain motifs in primordial protein folds	4
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	4
Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation	4
Analysis of CheW‐like domains provides insights into organization of prokaryotic chemotaxis systems	4
A Maximum Caliber analysis of the Foldon Hypothesis	4
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	4
Remarked suppression of Aβ42 protomer–protomer dissociation reaction elucidated by molecular dynamics simulation	4
Antibody mutations favoring pH‐dependent binding in solid tumor microenvironments: Insights from large‐scale structure‐based calculations	4
Annexin A1, A2, A5, and A6 involvement in human pathologies	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
A new method for protein characterization and classification using geometrical features for 3D face analysis: An example of tubulin structures	4
Common mechanism of thermostability in small α‐ and β‐proteins studied by molecular dynamics	4
Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol‐phosphate dehydratase	4
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	4
DeepCys: Structure‐based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains	4
Structural dynamics of pentapeptide repeat proteins	4
The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing	4
Protein oligomer structure prediction using GALAXY in CASP14	4
Introduction of a new scheme for classifying β‐turns in protein structures	4
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	4