Research graph
References from Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Local targets link to admitted publications; unresolved targets remain external evidence.
Recent advances in user-friendly computational tools to engineer protein function
2020 · External reference
10.1016/j.csbj.2017.07.002 · Admitted local publication
Unresolved reference
2016 · External reference
10.1002/cctc.201300950
10.1002/cctc.201300950 · External reference
10.1038/nrg3414
10.1038/nrg3414 · External reference
Correlated mutations: a hallmark of phenotypic amino acid substitutions
10.1371/journal.pcbi.1000923 · 2010 · External reference
Practical analysis of specificity-determining residues in protein families
10.1093/bib/bbv045 · 2016 · External reference
10.1002/biot.201400150
10.1002/biot.201400150 · External reference
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10.1006/jmbi.1996.0167 · External reference
A method to predict functional residues in proteins
10.1038/nsb0295-171 · 1995 · External reference
10.1016/s0022-2836(02)00587-9
10.1016/s0022-2836(02)00587-9 · External reference
Prediction of Protein-Ligand Interaction Based on the Positional Similarity Scores Derived from Amino Acid Sequences
10.3390/ijms21010024 · 2020 · External reference
10.1110/ps.03191704
10.1110/ps.03191704 · External reference
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies
10.1093/nar/gkaa276 · 2020 · External reference
10.1039/c6cc06055b
10.1039/c6cc06055b · External reference
Computational tools for designing and engineering enzymes
10.1016/j.cbpa.2013.12.003 · 2014 · External reference
10.1016/j.enzmictec.2020.109632
10.1016/j.enzmictec.2020.109632 · External reference
10.1007/s12275-018-7483-y
10.1007/s12275-018-7483-y · External reference
10.1371/journal.pone.0177392
10.1371/journal.pone.0177392 · External reference
10.1002/ange.201810005
10.1002/ange.201810005 · External reference
Ligand-based modeling for the prediction of pharmacophore features for multi-targeted inhibition of the arachidonic acid cascade
10.1002/minf.201700073 · 2018 · External reference
10.1016/j.csbj.2014.09.001 · Admitted local publication
10.1093/nar/gky1004
10.1093/nar/gky1004 · External reference
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems
10.1093/bioinformatics/btz224 · 2019 · External reference
10.1039/c8cc02426j
10.1039/c8cc02426j · External reference
10.1021/acs.chemrev.5b00562
10.1021/acs.chemrev.5b00562 · External reference
10.1371/journal.pcbi.1005398
10.1371/journal.pcbi.1005398 · External reference
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins
10.1142/s0219720020400119 · 2020 · External reference
10.1016/j.drudis.2016.11.001
10.1016/j.drudis.2016.11.001 · External reference
10.1002/pro.3274
10.1002/pro.3274 · External reference
10.1093/database/baw038
10.1093/database/baw038 · External reference
10.1093/bioinformatics/btr168
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10.1016/0263-7855(96)00018-5
10.1016/0263-7855(96)00018-5 · External reference
10.1016/j.csbj.2020.03.011 · Admitted local publication
10.1093/bioinformatics/btz236
10.1093/bioinformatics/btz236 · External reference
Critical assessment of structure-based sequence alignment methods at distant relationships
10.1093/bib/bbq025 · 2011 · External reference
10.1371/journal.pcbi.0040010
10.1371/journal.pcbi.0040010 · External reference
MAFFT-DASH: integrated protein sequence and structural alignment
2019 · External reference
Mustguseal: a server for multiple structure-guided sequence alignment of protein families
10.1093/bioinformatics/btx831 · 2018 · External reference
10.1093/nar/gkn072
10.1093/nar/gkn072 · External reference
Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families
10.1093/nar/gkz385 · 2019 · External reference
10.1093/nar/gky417
10.1093/nar/gky417 · External reference
PSSweb: protein structural statistics web server
10.1093/nar/gkw332 · 2016 · External reference
visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level
10.1186/s12859-020-3347-7 · 2020 · External reference
Lib ME—automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein–ligand recognition
10.1002/2211-5463.12150 · 2016 · External reference
10.1007/978-94-024-1069-3_11
10.1007/978-94-024-1069-3_11 · 2017 · External reference
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures
10.1093/nar/gks401 · 2012 · External reference
PDBSite: a database of the 3D structure of protein functional sites
2005 · External reference
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content
10.1093/nar/gkz456 · 2019 · External reference
Geometricus represents protein structures as shape-mers derived from moment invariants
10.1093/bioinformatics/btaa839 · 2020 · External reference
10.1107/s0907444904026460
10.1107/s0907444904026460 · External reference
10.1007/978-1-0716-1036-7_12
10.1007/978-1-0716-1036-7_12 · External reference
Catalytic and Lectin Domains in Neuraminidase A from Streptococcus pneumoniae are Capable of an Intermolecular Assembly: Implications for Biofilm Formation
10.1111/febs.15610 · 2021 · External reference
Bioinformatic analysis of the fold type I PLP-dependent enzymes reveals determinants of reaction specificity in l-threonine aldolase from Aeromonas jandaei
10.1002/2211-5463.12441 · 2018 · External reference
10.1111/febs.14486
10.1111/febs.14486 · External reference
10.1007/s00216-013-7068-x
10.1007/s00216-013-7068-x · External reference
10.1111/j.1747-0285.2007.00614.x
10.1111/j.1747-0285.2007.00614.x · External reference
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
10.1021/ja0723535 · 2007 · External reference
10.1038/nature05114
10.1038/nature05114 · External reference
10.1016/j.tim.2014.01.010
10.1016/j.tim.2014.01.010 · External reference
Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase
10.1007/s10822-013-9675-1 · 2013 · External reference
10.1371/journal.pcbi.1000939
10.1371/journal.pcbi.1000939 · External reference
Induced opening of influenza virus neuraminidase N2 150-loop suggests an important role in inhibitor binding
10.1038/srep01551 · 2013 · External reference
Mechanism of 150-cavity formation in influenza neuraminidase
10.1038/ncomms1390 · 2011 · External reference
Evolution of Substrate Specificity within a Diverse Family of β/α-Barrel-fold Basic Amino Acid Decarboxylases
10.1074/jbc.m110.121137 · 2010 · External reference
10.1074/jbc.m704066200
10.1074/jbc.m704066200 · External reference
Modular exchange of substrate-binding loops alters both substrate and cofactor specificity in a member of the aldo-keto reductase superfamily
10.1093/protein/gzs095 · 2013 · External reference
Unresolved reference
External reference
A novel polyester hydrolase from the marine bacterium Pseudomonas aestusnigri–Structural and functional insights
10.3389/fmicb.2020.00114 · 2020 · External reference
10.1073/pnas.0811070106
10.1073/pnas.0811070106 · External reference
10.1016/s0092-8674(02)00741-9
10.1016/s0092-8674(02)00741-9 · External reference
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding
10.1038/s41467-017-02258-w · 2017 · External reference
10.1073/pnas.1817455116
10.1073/pnas.1817455116 · External reference
The reaction mechanism of metallo-β-lactamases is tuned by the conformation of an active-site mobile loop
10.1128/aac.01754-18 · 2019 · External reference
The role of active site flexible loops in catalysis and of zinc in conformational stability of Bacillus cereus 569/H/9 β-lactamase
10.1074/jbc.m116.719005 · 2016 · External reference
10.1515/hsz-2018-0348
10.1515/hsz-2018-0348 · External reference
10.3390/molecules24030637
10.3390/molecules24030637 · External reference
10.1039/c6me00083e
10.1039/c6me00083e · External reference
pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families
10.1093/nar/gku448 · 2014 · External reference
Identifying pseudoenzymes using functional annotation. How loss of function correlates with mutations in the catalytic site
2019 · External reference
10.1111/febs.15199
10.1111/febs.15199 · External reference
10.1088/1757-899x/336/1/012017
10.1088/1757-899x/336/1/012017 · External reference
10.21105/joss.00205 · Admitted local publication
10.1145/304181.304187
10.1145/304181.304187 · External reference
DBSCAN revisited, revisited: why and how you should (still) use DBSCAN
10.1145/3068335 · 2017 · External reference
10.1016/0377-0427(87)90125-7
10.1016/0377-0427(87)90125-7 · External reference
10.1093/nar/gkv1316
10.1093/nar/gkv1316 · External reference
Human p38α Mitogen-Activated Protein Kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod
10.1080/07391102.2018.1475260 · 2019 · External reference
Supercomputer Lomonosov-2: large scale, deep monitoring and fine analytics for the user community
2019 · External reference
