Proteins-Structure Function and Bioinformatics

Papers
(The TQCC of Proteins-Structure Function and Bioinformatics is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-07-01 to 2024-07-01.)
ArticleCitations
Critical assessment of methods of protein structure prediction (CASP)—Round XIV306
Applying and improving AlphaFold at CASP14248
High‐accuracy protein structure prediction in CASP14233
Human SARS CoV‐2 spike protein mutations145
Multi‐state modeling of G‐protein coupled receptors at experimental accuracy97
Plastics degradation by hydrolytic enzymes: The plastics‐active enzymes database—PAZy93
Perturbing the energy landscape for improved packing during computational protein design92
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment76
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges48
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP1448
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods46
Assessing the utility of CASP14 models for molecular replacement42
Assessment of the CASP14 assembly predictions39
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP1439
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination36
Assessment of thePETaseconformational changes induced by poly(ethylene terephthalate) binding35
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain34
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
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes33
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold232
Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases30
Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor30
Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?29
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease29
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures28
Assessment of three‐dimensional RNA structure prediction in CASP1528
When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14—(tFold for CASP14 contact prediction)27
New prediction categories in CASP1527
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning27
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP27
Target highlights in CASP14: Analysis of models by structure providers26
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic26
Evolutionary relationships and sequence‐structure determinants in human SARS coronavirus‐2 spike proteins for host receptor recognition25
Predicting protein flexibility with AlphaFold24
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction23
Recent progress in the structural biology of P2X receptors23
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐223
Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment22
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins22
Why are ACE2 binding coronavirus strains SARS‐CoV/SARS‐CoV‐2 wild and NL63 mild?22
Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome21
ACE2‐based decoy receptors for SARS coronavirus 221
Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism21
Evaluation of model refinement in CASP1420
Physics‐based protein structure refinement in the era of artificial intelligence20
Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer19
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP1519
Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations18
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment18
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP1418
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro18
A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains17
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability17
Molecular dynamics simulations identify the regions of compromised thermostability in SazCA16
Critical assessment of methods of protein structure prediction (CASP)—Round XV16
Tertiary structure assessment at CASP1516
Improved multimer prediction using massive sampling with AlphaFold in CASP1516
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐1916
Protein oligomer modeling guided by predicted interchain contacts in CASP1416
SidechainNet: An all‐atom protein structure dataset for machine learning15
Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 215
Assessing the accuracy of contact and distance predictions in CASP1415
RNA target highlights in CASP15: Evaluation of predicted models by structure providers15
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots14
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP1414
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction14
New amino acid substitution matrix brings sequence alignments into agreement with structure matches14
PDB‐tools web: A user‐friendly interface for the manipulation of PDB files14
Biological nanopores for sensing applications14
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling14
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins13
Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker13
Comparative protein structure network analysis on 3CLpro from SARS‐CoV‐1 and SARS‐CoV‐213
From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation13
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP1513
High‐resolution structure of a partially folded insulin aggregation intermediate13
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses13
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction13
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes13
Genome‐wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights12
Exploring the structure and dynamics of proteins in soil organic matter12
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma12
Expansin Engineering Database: A navigation and classification tool for expansins and homologues11
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses11
Using normal mode analysis on protein structural models. How far can we go on our predictions?11
Insights into the mechanisms of light‐oxygen‐voltage domain color tuning from a set of high‐resolution X‐ray structures11
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments11
Estimation of model accuracy in CASP15 using the ModFOLDdock server10
Cryo‐EM targets in CASP1410
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions10
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images10
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)10
Assessment of protein–ligand complexes in CASP1510
Assessing the binding properties of CASP14 targets and models10
Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH10
Mapping of antibody epitopes based on docking and homology modeling10
RNA tertiary structure prediction using RNAComposer in CASP159
Protein target highlights in CASP15: Analysis of models by structure providers9
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring9
Assessment of the assessment—All about complexes9
Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation9
RNA tertiary structure modeling with BRiQ potential in CASP159
Protein structure search to support the development of protein structure prediction methods9
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms9
The effect of lipid composition on the dynamics of tau fibrils9
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors9
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network9
Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution9
Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean9
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study9
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors9
Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB9
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum9
Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes9
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing9
Plastic structures for diverse substrates: A revisit of human ABC transporters9
RF‐SVM: Identification of DNA‐binding proteins based on comprehensive feature representation methods and support vector machine8
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides8
Structural compliance: A new metric for protein flexibility8
Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures8
Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding8
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins8
From propensities to patterns to principles in protein folding8
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc428
Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin8
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery8
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP158
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics study8
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 analysis7
Calcium inhibits penetration of Alzheimer's Aβ142 monomers into the membrane7
Ca2+ as cofactor of the mitochondrial H+‐translocating F1FO‐ATP(hydrol)ase7
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP157
A rod conformation of the Pyrococcus furiosus Rad50 coiled coil7
Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites7
Performance of human and server prediction in CAPRI rounds 38‐457
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts7
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces7
Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor7
Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis7
A detailed mapping of the readily accessible disulphide bonds in the cortex of wool fibres7
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands7
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches6
Proteome analysis of the circadian clock protein PERIOD26
A computer aided drug discovery based discovery of lead‐like compounds against KDM5A for cancers using pharmacophore modeling and high‐throughput virtual screening6
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP156
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study6
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP156
Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis6
Consistency and variation of protein subcellular location annotations6
Novel antimicrobial anionic cecropins from the spruce budworm feature a poly‐L‐aspartic acid C‐terminus6
The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors6
Circuit topology predicts pathogenicity of missense mutations6
Conserved internal hydration motifs in protein kinases6
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins6
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?6
Structures and interactions of insulin‐like peptides from cone snail venom6
The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils6
ANOVA‐particle swarm optimization‐based feature selection and gradient boosting machine classifier for improved protein–protein interaction prediction6
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks6
Predicting mutant outcome by combining deep mutational scanning and machine learning6
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions6
Are granulins copper sequestering proteins?6
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues6
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium6
A geometrical framework for thinking about proteins6
Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation6
Introduction of a new scheme for classifying β‐turns in protein structures6
Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide5
The X‐ray crystal structure of human A15C neuroglobin reveals both native/de novo disulfide bonds and unexpected ligand‐binding sites5
Conformational changes in a Vernier zone region: Implications for antibody dual specificity5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains5
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks5
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning5
Total free energy analysis of fully hydrated proteins5
Study on functional sites in human multidrug resistance protein 1 (hMRP1)5
MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH5
Exploring CCRL2 chemerin binding using accelerated molecular dynamics5
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins5
Ligand Binding Site ComparisonLiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites5
Further thermo‐stabilization of thermophilic rhodopsin from Thermus thermophilusJL‐18 through engineering in extramembrane regions5
Dihydrolipoamide dehydrogenase moonlighting activity as a DNA chelating agent5
Protein dynamics analysis identifies candidate cancer driver genes and mutations in TCGA data5
Do “Newly Born” orphan proteins resemble “Never Born” proteins? A study using three deep learning algorithms5
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase5
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps5
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors5
PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints5
Protein folding and unfolding: proline cistrans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel5
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding5
Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF25
Sequence and evolutionary analysis of bacterial ribosomal S1 proteins5
Automated benchmarking of combined protein structure and ligand conformation prediction5
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii5
Inhibition of Mycobacterium tuberculosisInhA by 3‐nitropropanoic acid5
New tyrosinases with putative action against contaminants of emerging concern5
Tuning the binding interface between Machupo virus glycoprotein and human transferrin receptor5
Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers?5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP155
Simplified geometric representations of protein structures identify complementary interaction interfaces5
Distinctive communication networks in inactive states of β2‐adrenergic receptor: Mutual information and entropy transfer analysis5
Protein oligomer structure prediction using GALAXY in CASP145
Inferring metal binding sites in flexible regions of proteins5
Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target5
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence5
Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase5
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane5
Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B5
β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils5
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set5
Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods5
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