Comparative Protein Structure Modeling Using MODELLER.

PubWeight™: 0.95‹?› | Rank: Top 15%

🔗 View Article (PMID 27322406)

Published in Curr Protoc Bioinformatics on June 20, 2016

Authors

Benjamin Webb1, Andrej Sali1

Author Affiliations

1: University of California at San Francisco, San Francisco, California.

Articles citing this

Clinical, genetic, and structural basis of congenital adrenal hyperplasia due to 11β-hydroxylase deficiency. Proc Natl Acad Sci U S A (2017) 0.82

Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating. Elife (2017) 0.82

Structure of the transporter associated with antigen processing trapped by herpes simplex virus. Elife (2016) 0.78

A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure. Immunity (2017) 0.78

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol (2017) 0.77

Characterization of BRPMBL, the bleomycin-resistance protein associated with the carbapenemase NDM. Antimicrob Agents Chemother (2017) 0.76

Modeling disordered protein interactions from biophysical principles. PLoS Comput Biol (2017) 0.76

Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail. Elife (2017) 0.75

Meprin Metalloproteases Generate Biologically Active Soluble Interleukin-6 Receptor to Induce Trans-Signaling. Sci Rep (2017) 0.75

Implications of SDHB genetic testing in patients with sporadic pheochromocytoma. Langenbecks Arch Surg (2017) 0.75

Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene. PLoS One (2017) 0.75

APETx4, a Novel Sea Anemone Toxin and a Modulator of the Cancer-Relevant Potassium Channel KV10.1. Mar Drugs (2017) 0.75

Species specificity of vaccinia virus complement control protein towards bovine classical pathway is governed primarily by direct interaction of its acidic residues with factor I. J Virol (2017) 0.75

Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLoS One (2017) 0.75

The Influence of Disulfide Bonds on the Mechanical Stability of Proteins is Context Dependent. J Biol Chem (2017) 0.75

Articles cited by this

(truncated to the top 100)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol (1970) 155.96

Identification of common molecular subsequences. J Mol Biol (1981) 130.53

Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61

T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88

The Pfam protein families database. Nucleic Acids Res (2004) 56.46

Profile hidden Markov models. Bioinformatics (1998) 56.04

All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00

Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (2005) 34.83

MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34

Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc (2009) 32.64

Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57

Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26

SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res (2003) 25.86

Position-based sequence weights. J Mol Biol (1994) 24.41

The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92

The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68

Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29

The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58

A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol (1987) 19.30

Errors in protein structures. Nature (1996) 18.70

Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct (2000) 17.81

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97

SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21

TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15

A method to identify protein sequences that fold into a known three-dimensional structure. Science (1991) 14.08

InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45

Assessment of protein models with three-dimensional profiles. Nature (1992) 12.64

Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol (2000) 12.05

Protein structure prediction and structural genomics. Science (2001) 11.76

Ensembl 2013. Nucleic Acids Res (2012) 11.70

The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61

GenBank. Nucleic Acids Res (2012) 10.89

Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol (2000) 10.87

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol (2001) 10.02

Twilight zone of protein sequence alignments. Protein Eng (1999) 9.83

Modeling of loops in protein structures. Protein Sci (2000) 9.68

Recognition of errors in three-dimensional structures of proteins. Proteins (1993) 9.38

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res (2007) 9.16

SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09

Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35

Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins (2000) 8.17

The PROSITE database. Nucleic Acids Res (2006) 8.11

Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci (1993) 7.90

The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res (2005) 7.66

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40

Using known substructures in protein model building and crystallography. EMBO J (1986) 7.36

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A (1998) 7.18

PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16

Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol (2003) 7.15

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods (2009) 6.77

The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr (2004) 6.49

A comparison of scoring functions for protein sequence profile alignment. Bioinformatics (2004) 6.44

Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol (1987) 6.42

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol (1999) 6.42

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol (1990) 6.08

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06

Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins (2003) 5.88

Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol (1994) 5.76

Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res (1996) 5.68

Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res (2005) 5.59

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci (2002) 5.47

Comparative model-building of the mammalian serine proteases. J Mol Biol (1981) 5.42

Conformations of immunoglobulin hypervariable regions. Nature (1990) 5.31

A hierarchical approach to all-atom protein loop prediction. Proteins (2004) 5.18

Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08

Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell (2001) 5.01

FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins (2001) 4.85

MUSTANG: a multiple structural alignment algorithm. Proteins (2006) 4.69

Assessing protein structures with a non-local atomic interaction energy. J Mol Biol (1998) 4.42

Accurate modeling of protein conformation by automatic segment matching. J Mol Biol (1992) 4.39

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A (1998) 4.17

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A (1984) 4.08

Knowledge-based potentials for proteins. Curr Opin Struct Biol (1995) 3.94

FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res (2010) 3.91

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol (1991) 3.81

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng (1989) 3.79

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res (2006) 3.76

Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics (2003) 3.70

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol (2005) 3.69

Template-based protein structure modeling using the RaptorX web server. Nat Protoc (2012) 3.68

Tools for comparative protein structure modeling and analysis. Nucleic Acids Res (2003) 3.68

A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38

ModLoop: automated modeling of loops in protein structures. Bioinformatics (2003) 3.31

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods (2009) 3.25

Identification of related proteins on family, superfamily and fold level. J Mol Biol (2000) 3.24

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A (2002) 3.23

Articles by these authors

Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2014) 2.17

Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Protein Sci (2016) 0.79