Comparative Protein Structure Modeling Using MODELLER (Q30366550)

21 June 2017

Comparative Protein Structure Modeling Using MODELLER. (English)

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21 June 2017

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Andrej Sali

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author name string

Benjamin Webb

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1

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21 June 2017

8 September 2014

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21 June 2017

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21 June 2017

47

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Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

21 June 2017

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

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SCOP database in 2004: refinements integrate structure and sequence family data

21 January 2018

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Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

21 January 2018

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The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

21 January 2018

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21 January 2018

The Protein Model Portal

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Secondary structure formation in model polypeptide chains.

21 January 2018

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The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012

21 January 2018

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The Universal Protein Resource (UniProt)

21 January 2018

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Protein structure prediction and structural genomics

21 January 2018

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A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons

21 January 2018

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The Pfam protein families database

21 January 2018

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Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

21 January 2018

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Toward the estimation of the absolute quality of individual protein structure models

21 January 2018

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21 January 2018

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21 January 2018

The Protein Data Bank

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Knowledge-based prediction of protein structures and the design of novel molecules

21 January 2018

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A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

21 January 2018

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Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm

21 January 2018

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Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

21 January 2018

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Inference of functional properties from large-scale analysis of enzyme superfamilies

21 January 2018

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A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme

21 January 2018

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The ProDom database of protein domain families: more emphasis on 3D

21 January 2018

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Prediction of local structure in proteins using a library of sequence-structure motifs

21 January 2018

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Conformations of immunoglobulin hypervariable regions

21 January 2018

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Modelling the polypeptide backbone with 'spare parts' from known protein structures

21 January 2018

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CaspR: a web server for automated molecular replacement using homology modelling

21 January 2018

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Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin

21 January 2018

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Modeling of protein loops by simulated annealing

21 January 2018

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Verification of protein structures: patterns of nonbonded atomic interactions

21 January 2018

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CODA: a combined algorithm for predicting the structurally variable regions of protein models.

21 January 2018

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Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

21 January 2018

1 reference

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Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

21 January 2018

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A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

21 January 2018

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Optimized atomic statistical potentials: assessment of protein interfaces and loops

21 January 2018

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MASS: multiple structural alignment by secondary structures

21 January 2018

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Profile hidden Markov models

21 January 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

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A comparison of scoring functions for protein sequence profile alignment.

21 January 2018

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Structure-based approach for the discovery of bis-benzamidines as novel inhibitors of matriptase

21 January 2018

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How well can the accuracy of comparative protein structure models be predicted?

21 January 2018

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Tools for comparative protein structure modeling and analysis

21 January 2018

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Saturating representation of loop conformational fragments in structure databanks

21 January 2018

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Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.

21 January 2018

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Comparison of systematic search and database methods for constructing segments of protein structure

21 January 2018

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Protein structure modeling in the proteomics era.

21 January 2018

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Modeller: generation and refinement of homology-based protein structure models

21 January 2018

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ModLoop: automated modeling of loops in protein structures

21 January 2018

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Modeling of loops in protein structures

21 January 2018

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Evolution and physics in comparative protein structure modeling.

21 January 2018

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21 January 2018

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Study of the structural dynamics of the E coli 70S ribosome using real-space refinement

21 January 2018

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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

21 January 2018

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Profile analysis: detection of distantly related proteins

21 January 2018

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Novel protein folds and their nonsequential structural analogs

21 January 2018

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The Protein Model Portal--a comprehensive resource for protein structure and model information

21 January 2018

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A new method for building protein conformations from sequence alignments with homologues of known structure

21 January 2018

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Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

21 January 2018

1 reference

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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.

21 January 2018

1 reference

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Errors in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Structure determination of turkey egg-white lysozyme using Laue diffraction data

21 January 2018

1 reference

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Integration of bioinformatics resources for functional analysis of gene expression and proteomic data

21 January 2018

1 reference

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21 January 2018

The PROSITE database.

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InterPro in 2011: new developments in the family and domain prediction database

21 January 2018

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A hierarchical approach to all-atom protein loop prediction

21 January 2018

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FFAS03: a server for profile--profile sequence alignments

21 January 2018

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Comparative protein structure modeling by iterative alignment, model building and model assessment

21 January 2018

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GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

21 January 2018

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Evaluating the potential of using fold-recognition models for molecular replacement.

21 January 2018

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On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations

21 January 2018

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Template-based protein structure modeling using the RaptorX web server.

21 January 2018

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Swiss-PDB Viewer (Deep View).

21 January 2018

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Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry

21 January 2018

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LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

21 January 2018

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SAM-T08, HMM-based protein structure prediction.

21 January 2018

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Hidden Markov models for detecting remote protein homologies

21 January 2018

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Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

21 January 2018

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

21 January 2018

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Protein structure prediction on the Web: a case study using the Phyre server

21 January 2018

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Enhanced genome annotation using structural profiles in the program 3D-PSSM

21 January 2018

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A study of the evolution of inverted-topology repeats from LeuT-fold transporters using AlignMe.

21 January 2018

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The SWISS-MODEL Repository and associated resources

21 January 2018

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A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

21 January 2018

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MUSTANG: a multiple structural alignment algorithm.

21 January 2018

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Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

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Hidden Markov models in computational biology. Applications to protein modeling

21 January 2018

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PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

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21 January 2018

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SMART 7: recent updates to the protein domain annotation resource

21 January 2018

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Accurate modeling of protein conformation by automatic segment matching

21 January 2018

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Structure-based design of parasitic protease inhibitors

21 January 2018

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GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing

21 January 2018

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Identification of related proteins on family, superfamily and fold level.

21 January 2018

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A new progressive-iterative algorithm for multiple structure alignment.

21 January 2018

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Assessment of protein models with three-dimensional profiles

21 January 2018

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

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Variable gap penalty for protein sequence-structure alignment.

21 January 2018

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Alignment of multiple protein structures based on sequence and structure features.

21 January 2018

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Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

21 January 2018

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Comparative protein structure modeling of genes and genomes

21 January 2018

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DBAli: a database of protein structure alignments.

21 January 2018

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Reliability of assessment of protein structure prediction methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Alignment of protein sequences by their profiles

21 January 2018

1 reference

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Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans

21 January 2018

1 reference

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Improvement of the GenTHREADER method for genomic fold recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

The PSIPRED protein structure prediction server

21 January 2018

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Assessing protein structures with a non-local atomic interaction energy.

21 January 2018

1 reference

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Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.

21 January 2018

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Progress and challenges in high-resolution refinement of protein structure models.

21 January 2018

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Physically realistic homology models built with ROSETTA can be more accurate than their templates

21 January 2018

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lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.

21 January 2018

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A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding

21 January 2018

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A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

21 January 2018

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An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

21 January 2018

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

21 January 2018

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Critical assessment of methods of protein structure prediction - Round VIII.

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins.

21 January 2018

1 reference

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A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

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T-Coffee: A novel method for fast and accurate multiple sequence alignment

21 January 2018

1 reference

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Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

An automated classification of the structure of protein loops.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Structural Diversity in a Family of Homologous Proteins

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

PROMALS3D: a tool for multiple protein sequence and structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Protein structure prediction: inroads to biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

ModBase, a database of annotated comparative protein structure models, and associated resources

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Searching databases of conserved sequence regions by aligning protein multiple-alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Pre-calculated protein structure alignments at the RCSB PDB website

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Cysteine proteinases from distinct cellular compartments are recruited to phagocytic vesicles by Entamoeba histolytica

21 January 2018

1 reference

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Improved model quality assessment using ProQ2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Taxonomy and conformational analysis of loops in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Structure-based inhibitor design by using protein models for the development of antiparasitic agents

21 January 2018

1 reference

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The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

I-TASSER: a unified platform for automated protein structure and function prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Fold and function predictions for Mycoplasma genitalium proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Comparative protein modelling by satisfaction of spatial restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Derivation of rules for comparative protein modeling from a database of protein structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

A graph-theoretic algorithm for comparative modeling of protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Advances in comparative protein-structure modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Misleading local sequence alignments: implications for comparative protein modelling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

The importance of alignment accuracy for molecular replacement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

SWISS-MODEL: An automated protein homology-modeling server

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

A method for simultaneous alignment of multiple protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Optimization of multiple-sequence alignment based on multiple-structure alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Statistical potential for assessment and prediction of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Conformation of β-hairpins in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Recognition of errors in three-dimensional structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Knowledge-based potentials for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Identification of common molecular subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Protein homology detection by HMM-HMM comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

The HHpred interactive server for protein homology detection and structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

High-resolution comparative modeling with RosettaCM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Multiple protein structure alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Comparative modelling of major house dust mite allergen Der p I: structure validation using an extended environmental amino acid propensity table

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

A 3D building blocks approach to analyzing and predicting structure of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Protein docking for low-resolution structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

A molecular dynamics approach for the generation of complete protein structures from limited coordinate data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

PDB-based protein loop prediction: parameters for selection and methods for optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Scoring profile-to-profile sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

RAPTOR: optimal protein threading by linear programming

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Ligand specificity of brain lipid-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

TM-align: a protein structure alignment algorithm based on the TM-score

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Determining protein loop conformation using scaling-relaxation techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Long loop prediction using the protein local optimization program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI0506S47

10.1002/0471250953.BI0506S47

21 January 2018

Identifiers

DOI

1 reference

21 June 2017

1 reference

PubMed ID

25199792