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。Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
David M. Kristensen et al.
BMC BIOINFORMATICS (2008)
I-TASSER server for protein 3D structure prediction
Yang Zhang
BMC BIOINFORMATICS (2008)
Pfam 10 years on: 10 000 families and still growing
Stephen John Sammut et al.
BRIEFINGS IN BIOINFORMATICS (2008)
Evolution of protein domain promiscuity in eukaryotes
Malay Kumar Basu et al.
GENOME RESEARCH (2008)
Assessment of programs for ligand binding affinity prediction
Ryangguk Kim et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
Michal Brylinski et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
Mu Gao et al.
NUCLEIC ACIDS RESEARCH (2008)
De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features
R. Matthew Ward et al.
PLOS ONE (2008)
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
Ranyee A. Chiang et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Ranking predicted protein structures with support vector regression
Jian Qiu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
Michal Brylinski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
MIPS: analysis and annotation of genome information in 2007
H. W. Mewes et al.
NUCLEIC ACIDS RESEARCH (2008)
KEGG for linking genomes to life and the environment
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2008)
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2008)
Data growth and its impact on the SCOP database: new developments
Antonina Andreeva et al.
NUCLEIC ACIDS RESEARCH (2008)
Ab initio modeling of small proteins by iterative TASSER simulations
Sitao Wu et al.
BMC BIOLOGY (2007)
Advanced sequencing technologies and their wider impact in microbiology
Neil Hall
JOURNAL OF EXPERIMENTAL BIOLOGY (2007)
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
Sheng-You Huang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
SODOCK: Swarm optimization for highly flexible protein-ligand docking
Hung-Ming Chen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
Lesley H. Greene et al.
NUCLEIC ACIDS RESEARCH (2007)
High precision multi-genome scale reannotation of enzyme function by EFICAz
Adrian K. Arakaki et al.
BMC GENOMICS (2006)
Similarity-based virtual screening using 2D fingerprints
Peter Willett
DRUG DISCOVERY TODAY (2006)
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
Jens Meiler et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
A critical assessment of docking programs and scoring functions
Gregory L. Warren et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
Solution NMR in structural genomics
Adelinda Yee et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
Evolution of enzyme superfamilies
Margaret E. Glasner et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2006)
LIGSITEcsc:: predicting ligand binding sites using the Connolly surface and degree of conservation
Bingding Huang et al.
BMC STRUCTURAL BIOLOGY (2006)
The ancient Virus World and evolution of cells
Eugene V. Koonin et al.
BIOLOGY DIRECT (2006)
A metabolic network in the evolutionary context: Multiscale structure and modularity
Victor Spirin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
New avenues in protein function prediction
Iddo Friedberg et al.
PROTEIN SCIENCE (2006)
Efficient prediction of nucleic acid binding function from low-resolution protein structures
A Szilagyi et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
The proteome: structure, function and evolution
K Fleming et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)
Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications
John-Marc Chandonia et al.
BMC STRUCTURAL BIOLOGY (2006)
Automated discovery of 3D motifs for protein function annotation
BJ Polacco et al.
BIOINFORMATICS (2006)
Blind docking of drug-sized compounds to proteins with up to a thousand residues
C Hetényi et al.
FEBS LETTERS (2006)
A method for localizing ligand binding pockets in protein structures
F Glaser et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
The Universal Protein Resource (UniProt): an expanding universe of protein information
Cathy H. Wu et al.
NUCLEIC ACIDS RESEARCH (2006)
MODBASE: a database of annotated comparative protein structure models and associated resources
Ursula Pieper et al.
NUCLEIC ACIDS RESEARCH (2006)
Pfam: clans, web tools and services
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2006)
Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols
A Evers et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
Assignment of protein function in the postgenomic era
A Saghatelian et al.
NATURE CHEMICAL BIOLOGY (2005)
ProFunc: a server for predicting protein function from 3D structure
RA Laskowski et al.
NUCLEIC ACIDS RESEARCH (2005)
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
R Kolodny et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
A scoring function for docking ligands to low-resolution protein structures
E Bindewald et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Comparison of automated docking programs as virtual screening tools
MD Cummings et al.
JOURNAL OF MEDICINAL CHEMISTRY (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)
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity
JA Gerlt et al.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2005)
TM-align: a protein structure alignment algorithm based on the TM-score
Y Zhang et al.
NUCLEIC ACIDS RESEARCH (2005)
The PEDANT genome database in 2005
ML Riley et al.
NUCLEIC ACIDS RESEARCH (2005)
Microbial genomes have over 72% structure assignment by the threading algorithm PROSOPECTOR-Q
D Kihara et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
AK Arakaki et al.
BIOINFORMATICS (2004)
Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast
SM Baxter et al.
MOLECULAR & CELLULAR PROTEOMICS (2004)
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm
J Skolnick et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
E Perola et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Similarity search profiling reveals effects of fingerprint scaling in virtual screening
L Xue et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)
Assessing scoring functions for protein-ligand interactions
P Ferrara et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
JA Erickson et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
WD Tian et al.
NUCLEIC ACIDS RESEARCH (2004)
The KEGG resource for deciphering the genome
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2004)
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
E Kellenberger et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Automated prediction of protein function and detection of functional sites from structure
F Pazos et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Soft docking and multiple receptor conformations in virtual screening
AM Ferrari et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
Y Zhang et al.
BIOPHYSICAL JOURNAL (2004)
Automated structure prediction of weakly homologous proteins on a genomic scale'
Y Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
PREDICT modeling and in-silico screening for G-protein coupled receptors
S Shacham et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
S Jones et al.
NUCLEIC ACIDS RESEARCH (2003)
How well is enzyme function conserved as a function of pairwise sequence identity?
WD Tian et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
The COG database: an updated version includes eukaryotes
RL Tatusov et al.
BMC BIOINFORMATICS (2003)
Assessment of genome-wide protein function classification for Drosophila melanogaster
HY Mi et al.
GENOME RESEARCH (2003)
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
SL McGovern et al.
JOURNAL OF MEDICINAL CHEMISTRY (2003)
OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms
G Zehetner
NUCLEIC ACIDS RESEARCH (2003)
Implications of protein flexibility for drug discovery
SJ Teague
NATURE REVIEWS DRUG DISCOVERY (2003)
Annotation in three dimensions. PINTS: Patterns in non-homologous tertiary structures
A Stark et al.
NUCLEIC ACIDS RESEARCH (2003)
Definitions of enzyme function for the structural genomics era
PC Babbitt
CURRENT OPINION IN CHEMICAL BIOLOGY (2003)
Efficient identification of side-chain patterns using a multidimensional index tree
T Hamelryck
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Automatic methods for predicting functionally important residues
AD Mesa et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
An accurate, sensitive, and scalable method to identify functional sites in protein structures
H Yao et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Automatic prediction of protein function
B Rost et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2003)
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
A Yamaguchi et al.
NUCLEIC ACIDS RESEARCH (2003)
Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
C Bissantz et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Data mining the protein data bank: Residue interactions
TJ Oldfield
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
Analysis of catalytic residues in enzyme active sites
GJ Bartlett et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Function first: a powerful approach to post-genomic drug discovery
SF Betz et al.
DRUG DISCOVERY TODAY (2002)
Docking of small ligands to low-resolution and theoretically predicted receptor structures
M Wojciechowski et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
SB Pandit et al.
NUCLEIC ACIDS RESEARCH (2002)
Recognition templates for predicting adenylate-binding sites in proteins
SR Zhao et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Discovery of small-molecule inhibitors of bcl-2 through structure-based computer screening
IJ Enyedy et al.
JOURNAL OF MEDICINAL CHEMISTRY (2001)
THEMATICS: A simple computational predictor of enzyme function from structure
MJ Ondrechen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Prediction of functionally important residues based solely on the computed energetics of protein structure
AH Elcock
JOURNAL OF MOLECULAR BIOLOGY (2001)
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
TJA Ewing et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2001)
Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
CA Wilson et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Homology - a personal view on some of the problems
WM Fitch
TRENDS IN GENETICS (2000)
Structural genomics and its importance for gene function analysis
J Skolnick et al.
NATURE BIOTECHNOLOGY (2000)
KEGG: Kyoto Encyclopedia of Genes and Genomes
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2000)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)
From genes to protein structure and function: novel applications of computational approaches in the genomic era
J Skolnick et al.
TRENDS IN BIOTECHNOLOGY (2000)