相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
Vahid Mirjalili et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions
Jianyi Yang et al.
NUCLEIC ACIDS RESEARCH (2013)
SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
Eshel Faraggi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)
De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation
Meghan L. Bellows-Peterson et al.
JOURNAL OF MEDICINAL CHEMISTRY (2012)
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures
Jeffrey Skolnick et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Principles for designing ideal protein structures
Nobuyasu Koga et al.
NATURE (2012)
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation
Ambrish Roy et al.
NUCLEIC ACIDS RESEARCH (2012)
Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core
Grant S. Murphy et al.
STRUCTURE (2012)
Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement
Ambrish Roy et al.
STRUCTURE (2012)
Theoretical and Computational Protein Design
Ilan Samish et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 62 (2011)
Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations
Andrea Bazzoli et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement
Dong Xu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
CASP9 assessment of free modeling target predictions
Lisa Kinch et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Assessment of template based protein structure predictions in CASP9
Valerio Mariani et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling
Jian Zhang et al.
STRUCTURE (2011)
How significant is a protein structure similarity with TM-score=0.5?
Jinrui Xu et al.
BIOINFORMATICS (2010)
Discovery of Entry Inhibitors for HIV-1 via a New De Novo Protein Design Framework
M. L. Bellows et al.
BIOPHYSICAL JOURNAL (2010)
New Compstatin Variants through Two De Novo Protein Design Frameworks
M. L. Bellows et al.
BIOPHYSICAL JOURNAL (2010)
I-TASSER: a unified platform for automated protein structure and function prediction
Ambrish Roy et al.
NATURE PROTOCOLS (2010)
Sequence and structural analysis of two designed proteins with 88% identity adopting different folds
Saravanan K. Mani et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2010)
Estimation of the number of α-helical and β-strand segments in proteins using circular dichroism spectroscopy
Narasimha Sreerama et al.
PROTEIN SCIENCE (2010)
Protein structure prediction: when is it useful?
Yang Zhang
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
Mocr: A novel fusion tag for enhancing solubility that is compatible with structural biology applications
James DelProposto et al.
PROTEIN EXPRESSION AND PURIFICATION (2009)
Computational design of Candida boidinii xylose reductase for altered cofactor specificity
George A. Khoury et al.
PROTEIN SCIENCE (2009)
Improved prediction of protein side-chain conformations with SCWRL4
Georgii G. Krivov et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Evaluation of template-based models in CASP8 with standard measures
Domenico Cozzetto et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
I-TASSER: Fully automated protein structure prediction in CASP8
Yang Zhang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2
Ho Ki Fung et al.
BIOPHYSICAL JOURNAL (2008)
I-TASSER server for protein 3D structure prediction
Yang Zhang
BMC BIOINFORMATICS (2008)
Solution conformation, backbone dynamics and lipid interactions of the intrinsically unstructured malaria surface protein MSP2
Xuecheng Zhang et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Stabilizing ionic interactions in a full-consensus ankyrin repeat protein
Tobias Merz et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles
Abigail Go et al.
PROTEIN SCIENCE (2008)
The NMR solution structure of the artificial protein M7 matches the computationally designed model
Claudius Stordeur et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
Sitao Wu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design
Xiaozhen Hu et al.
STRUCTURE (2008)
Ab initio modeling of small proteins by iterative TASSER simulations
Sitao Wu et al.
BMC BIOLOGY (2007)
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design
Gautam Dantas et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Template-based modeling and free modeling by I-TASSER in CASP7
Yang Zhang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
IPRO: An iterative computational protein library redesign and optimization procedure
Manish C. Saraf et al.
BIOPHYSICAL JOURNAL (2006)
On the origin and highly likely completeness of single-domain protein structures
Y Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Advances in protein structure prediction and de novo protein design:: A review
CA Floudas et al.
CHEMICAL ENGINEERING SCIENCE (2006)
Determination of the folding of proteins as a function of denaturants, osmolytes or ligands using circular dichroism
Norma J. Greenfield
NATURE PROTOCOLS (2006)
The FoldX web server: an online force field
J Schymkowitz et al.
NUCLEIC ACIDS RESEARCH (2005)
Protein homology detection by HMM-HMM comparison
J Söding
BIOINFORMATICS (2005)
Recapitulation of protein family divergence using flexible backbone protein design
CT Saunders et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
The protein structure prediction problem could be solved using the current PDB library
Y Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
TM-align: a protein structure alignment algorithm based on the TM-score
Y Zhang et al.
NUCLEIC ACIDS RESEARCH (2005)
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
HL Chen et al.
NUCLEIC ACIDS RESEARCH (2005)
Theory of protein folding
JN Onuchic et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Scoring function for automated assessment of protein structure template quality
Y Zhang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
The Pfam protein families database
A Bateman et al.
NUCLEIC ACIDS RESEARCH (2004)
Design of a novel globular protein fold with atomic-level accuracy
B Kuhlman et al.
SCIENCE (2003)
Solution structure of a de novo protein from a designed combinatorial library
YN Wei et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
G Dantas et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
PISCES: a protein sequence culling server
GL Wang et al.
BIOINFORMATICS (2003)
Designed to be stable:: Crystal structure of a consensus ankyrin repeat protein
A Kohl et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Structure of a de novo designed protein model of radical enzymes
QH Dai et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Computational de novo design, and characterization of an A2B2 diiron protein
CM Summa et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
R Guerois et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
RX Wang et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2002)
Conformational properties of α-synuclein in its free and lipid-associated states
D Eliezer et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Native protein sequences are close to optimal for their structures
B Kuhlman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
分享论文
