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References from COMPUTER-AIDED PROTEIN DIRECTED EVOLUTION: A REVIEW OF WEB SERVERS, DATABASES AND OTHER COMPUTATIONAL TOOLS FOR PROTEIN ENGINEERING. Local targets link to admitted publications; unresolved targets remain external evidence.
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10.1146/annurev-biophys-042910-155245
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Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis
10.1021/bi200063a · 2011 · External reference
Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A
10.1002/cbic.201100600 · 2012 · External reference
10.1039/b600517a
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10.1038/nchembio.203 · External reference
Optimizing industrial enzymes by directed evolution
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10.1016/j.cbpa.2009.01.017
10.1016/j.cbpa.2009.01.017 · External reference
Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries
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10.1016/j.copbio.2005.06.004
10.1016/j.copbio.2005.06.004 · External reference
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10.1093/nar/gkn226
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Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment
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dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method
10.1016/j.molcatb.2012.04.018 · 2012 · External reference
Unresolved reference
External reference
When second best is good enough: another probabilistic look at saturation mutagenesis
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10.1016/j.jmb.2008.01.043 · External reference
Multiple protein sequence alignment
10.1016/j.sbi.2008.03.007 · 2008 · External reference
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10.1093/nar/gkn822 · External reference
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2010 · External reference
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HotSprint: database of computational hot spots in protein interfaces
10.1093/nar/gkm813 · 2008 · External reference
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10.1093/nar/gkp410
10.1093/nar/gkp410 · External reference
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
10.1093/nar/gkm382 · 2007 · External reference
Lipase Engineering Database: understanding and exploiting sequence-structure-function relationships
10.1016/s1381-1177(00)00092-8 · 2000 · External reference
The PHA Depolymerase Engineering Database: a systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases
10.1186/1471-2105-10-89 · 2009 · External reference
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases
2010 · External reference
10.1186/1471-2164-10-390
10.1186/1471-2164-10-390 · External reference
SHV Lactamase Engineering Database: a reconciliation tool for SHV beta-lactamases in public databases
10.1186/1471-2164-11-563 · 2010 · External reference
The Protein Mutant Database
10.1093/nar/27.1.355 · 1999 · External reference
ProTherm, thermodynamic database for proteins and mutants: developments in version 3.0
10.1093/nar/30.1.301 · 2002 · External reference
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10.1093/nar/28.1.283 · 2000 · External reference
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10.1093/nar/gkh082 · 2004 · External reference
10.1093/database/bas028
10.1093/database/bas028 · External reference
The alpha/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering
10.1002/cbic.201000213 · 2010 · External reference
The Lipase Engineering Database: a navigation and analysis tool for protein families
10.1093/nar/gkg015 · 2003 · External reference
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A
10.1186/1471-2164-11-123 · 2010 · External reference
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
10.1093/bioinformatics/bth284 · 2004 · External reference
The cytochrome P450 engineering database: Integration of biochemical properties
10.1186/1471-2091-10-27 · 2009 · External reference
Structural and functional restraints in the evolution of protein families and superfamilies
10.1042/bst0370727 · 2009 · External reference
3DLigandSite: predicting ligand-binding sites using similar structures
10.1093/nar/gkq406 · 2010 · External reference
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
10.1093/bioinformatics/btq100 · 2010 · External reference
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins
10.1093/nar/gks435 · 2012 · External reference
10.1093/bioinformatics/bts095
10.1093/bioinformatics/bts095 · External reference
Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces
2008 · External reference
ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures
10.1021/ci2005687 · 2012 · External reference
TRITON: in silico construction of protein mutants and prediction of their activities
10.1093/bioinformatics/16.9.845 · 2000 · External reference
TRITON: a graphical tool for ligand-binding protein engineering
10.1093/bioinformatics/btn344 · 2008 · External reference
10.1016/j.bpc.2010.02.004
10.1016/j.bpc.2010.02.004 · External reference
10.1093/nar/gkm423
10.1093/nar/gkm423 · External reference
10.1093/bioinformatics/btr484
10.1093/bioinformatics/btr484 · External reference
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
10.1093/nar/gkr356 · 2011 · External reference
SRide: a server for identifying stabilizing residues in proteins
10.1093/nar/gki409 · 2005 · External reference
10.1093/nar/gkm401
10.1093/nar/gkm401 · External reference
ConPlex: a server for the evolutionary conservation analysis of protein complex structures
10.1093/nar/gkq328 · 2010 · External reference
Protein stability, flexibility and function
10.1016/j.bbapap.2010.11.005 · 2011 · External reference
10.1007/s00018-009-0014-6
10.1007/s00018-009-0014-6 · External reference
10.1038/nature06522
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10.1016/j.tibs.2009.07.004
10.1016/j.tibs.2009.07.004 · External reference
10.1093/protein/gzr014
10.1093/protein/gzr014 · External reference
10.1016/j.cbpa.2010.08.012
10.1016/j.cbpa.2010.08.012 · External reference
10.1002/prot.22375
10.1002/prot.22375 · External reference
10.1093/nar/gkq369
10.1093/nar/gkq369 · External reference
10.1016/j.copbio.2009.07.006
10.1016/j.copbio.2009.07.006 · External reference
Geometry-based sampling of conformational transitions in proteins
10.1016/j.str.2007.09.017 · 2007 · External reference
FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins
10.6026/97320630003134 · 2008 · External reference
10.1146/annurev.biophys.093008.131258
10.1146/annurev.biophys.093008.131258 · External reference
10.1016/j.sbi.2005.08.007
10.1016/j.sbi.2005.08.007 · External reference
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems
10.1146/annurev-physchem-032210-103335 · 2011 · External reference
10.1016/s1359-0278(97)00024-2
10.1016/s1359-0278(97)00024-2 · External reference
10.1016/s0006-3495(01)76033-x
10.1016/s0006-3495(01)76033-x · External reference
10.1016/j.theochem.2008.09.024
10.1016/j.theochem.2008.09.024 · External reference
High-throughput modeling and analysis of protein structural dynamics
10.1093/bib/bbm014 · 2007 · External reference
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
10.1093/nar/gkh368 · 2004 · External reference
WEBnm@: a web application for normal mode analyses of proteins
10.1186/1471-2105-6-52 · 2005 · External reference
10.1093/bioinformatics/btp304
10.1093/bioinformatics/btp304 · External reference
HingeProt: automated prediction of hinges in protein structures
10.1002/prot.21613 · 2008 · External reference
10.1002/(sici)1097-0134(19980201)30:2<144::aid-prot4>3.0.co;2-n
10.1002/(sici)1097-0134(19980201)30:2<144::aid-prot4>3.0.co;2-n · External reference
Database of ligand-induced domain movements in enzymes
10.1186/1472-6807-9-13 · 2009 · External reference
A method for the analysis of domain movements in large biomolecular complexes
10.1002/prot.22339 · 2009 · External reference
10.1038/nchem.1244
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10.1073/pnas.0909150106 · External reference
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10.1016/j.str.2005.10.007
10.1016/j.str.2005.10.007 · External reference
10.1016/j.str.2008.09.012
10.1016/j.str.2008.09.012 · External reference
Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
10.1002/prot.21899 · 2008 · External reference
In the light of directed evolution: pathways of adaptive protein evolution
10.1073/pnas.0901522106 · 2009 · External reference
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10.1093/bioinformatics/btm344
10.1093/bioinformatics/btm344 · External reference
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
10.1093/nar/gki375 · 2005 · External reference
10.1002/prot.20810
10.1002/prot.20810 · External reference
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
10.1093/bioinformatics/btm100 · 2007 · External reference
10.1093/bioinformatics/btp370
10.1093/bioinformatics/btp370 · External reference
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
10.1093/bioinformatics/btr576 · 2011 · External reference
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data
10.1093/nar/gkq528 · 2010 · External reference
10.1093/nar/gkr363
10.1093/nar/gkr363 · External reference
10.1186/1471-2105-12-151
10.1186/1471-2105-12-151 · External reference
10.1093/bioinformatics/btr254
10.1093/bioinformatics/btr254 · External reference
Integrated prediction of the effect of mutations on multiple protein characteristics
10.1002/prot.22870 · 2011 · External reference
CUPSAT: prediction of protein stability upon point mutations
10.1093/nar/gkl190 · 2006 · External reference
10.1093/bioinformatics/btn353
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10.1093/protein/gzq042
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