4.8 Article

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

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。
Article Biophysics

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Dina Schneidman-Duhovny et al.

BIOPHYSICAL JOURNAL (2013)

Article Biochemistry & Molecular Biology

Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology

Catharina Steentoft et al.

EMBO JOURNAL (2013)

Article Chemistry, Physical

Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes

Krishnakumar M. Ravikumar et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Biochemistry & Molecular Biology

Impact of Mutations on the Allosteric Conformational Equilibrium

Patrick Weinkam et al.

JOURNAL OF MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

Ursula Pieper et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

The RCSB Protein Data Bank: new resources for research and education

Peter W. Rose et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Mathematical & Computational Biology

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

Juergen Haas et al.

Database-The Journal of Biological Databases and Curation (2013)

Article Biochemical Research Methods

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

Francisco Martinez-Jimenez et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Chemistry, Multidisciplinary

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials

Haiguang Liu et al.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2012)

Article Biochemical Research Methods

A method for integrative structure determination of protein-protein complexes

Dina Schneidman-Duhovny et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

SALIGN: a web server for alignment of multiple protein sequences and structures

Hannes Braberg et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

A catalogue of putative HIV-1 protease host cell substrates

Francis Impens et al.

BIOLOGICAL CHEMISTRY (2012)

Article Biochemical Research Methods

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

Michael Remmert et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Structure-based model of allostery predicts coupling between distant sites

Patrick Weinkam et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Small Angle X-ray Scattering as a Complementary Tool for High-Throughput Structural Studies

Thomas D. Grant et al.

BIOPOLYMERS (2011)

Article Biochemical Research Methods

Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction

Tianyun Liu et al.

COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2011)

Article Chemistry, Medicinal

Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions

Hao Fan et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Biochemistry & Molecular Biology

Macromolecular docking restrained by a small angle X-ray scattering profile

Dina Schneidman-Duhovny et al.

JOURNAL OF STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Ursula Pieper et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

genenames.org: the HGNC resources in 2011

Ruth L. Seal et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Ongoing and future developments at the Universal Protein Resource

Rolf Apweiler et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Frederic Poitevin et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

Dominik Gront et al.

PLOS ONE (2011)

Review Chemistry, Medicinal

Template-Based Protein Modeling: Recent Methodological Advances

Pankaj R. Daga et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)

Article Biotechnology & Applied Microbiology

Emerging principles in protease-based drug discovery

Marcin Drag et al.

NATURE REVIEWS DRUG DISCOVERY (2010)

Article Biochemistry & Molecular Biology

The UCSC Genome Browser database: update 2010

Brooke Rhead et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

FoXS: a web server for rapid computation and fitting of SAXS profiles

Dina Schneidman-Duhovny et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution

Parthasarathy Sampathkumar et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Structure and flexibility within proteins as identified through small angle X-ray scattering

Martin Pelikan et al.

GENERAL PHYSIOLOGY AND BIOPHYSICS (2009)

Article Biochemistry & Molecular Biology

The completion of the Mammalian Gene Collection (MGC)

Gary Temple et al.

GENOME RESEARCH (2009)

Article Biochemical Research Methods

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

Greg L. Hura et al.

NATURE METHODS (2009)

Article Biochemistry & Molecular Biology

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

Ursula Pieper et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

InterPro: the integrative protein signature database

Sarah Hunter et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

HIV-1 Protease Inhibits Cap- and Poly(A)-Dependent Translation upon eIF4GI and PABP Cleavage

Alfredo Castello et al.

PLOS ONE (2009)

Article Biochemistry & Molecular Biology

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

Paul C. Whitford et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

Editorial Material Biochemistry & Molecular Biology

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

Torsten Schwede et al.

STRUCTURE (2009)

Article Biochemical Research Methods

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

John A. Capra et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Infectious Diseases

A Kernel for Open Source Drug Discovery in Tropical Diseases

Leticia Orti et al.

PLOS NEGLECTED TROPICAL DISEASES (2009)

Article Biotechnology & Applied Microbiology

Genomic-scale prioritization of drug targets: the TDR Targets database

Fernan Agueero et al.

NATURE REVIEWS DRUG DISCOVERY (2008)

Article Biochemistry & Molecular Biology

NCBIBLAST: a better web interface

Mark Johnson et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

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

David Eramian et al.

PROTEIN SCIENCE (2008)

Article Biochemistry & Molecular Biology

Remediation of the protein data bank archive

Kim Henrick et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Fold assessment for comparative protein structure modeling

Francisco Melo et al.

PROTEIN SCIENCE (2007)

Review Biochemistry & Molecular Biology

Analysis of X-ray and neutron scattering from biomacromolecular solutions

Maxim V. Petoukhov et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

FireDock: Fast interaction refinement in molecular docking

Nelly Andrusier et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

DBAli tools: mining the protein structure space

Marc A. Marti-Renom et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

ZRANK: Reranking protein docking predictions with an optimized energy function

Brian Pierce et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Biotechnology & Applied Microbiology

h0RFeome v3.1: A resource of human open reading frames representing over 10,000 human genes

Philippe Lamesch et al.

GENOMICS (2007)

Review Biochemistry & Molecular Biology

Statistical potential for assessment and prediction of protein structures

Min-Yi Shen et al.

PROTEIN SCIENCE (2006)

Article Multidisciplinary Sciences

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

Kei-ichi Okazaki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

The Universal Protein Resource (UniProt): an expanding universe of protein information

Cathy H. Wu et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

MODBASE: a database of annotated comparative protein structure models and associated resources

Ursula Pieper et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

All are not equal: A benchmark of different homology modeling programs

B Wallner et al.

PROTEIN SCIENCE (2005)

Article Biochemical Research Methods

PIBASE: a comprehensive database of structurally defined protein interfaces

FP Davis et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Protein homology detection by HMM-HMM comparison

J Söding

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

A highly sensitive selection method for directed evolution of homing endonucleases

ZL Chen et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

A hierarchical approach to all-atom protein loop prediction

MP Jacobson et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Alignment of protein sequences by their profiles

MA Marti-Renom et al.

PROTEIN SCIENCE (2004)

Article Biochemistry & Molecular Biology

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential

C Zhang et al.

PROTEIN SCIENCE (2004)

Article Biochemical Research Methods

The DISOPRED server for the prediction of protein disorder

JJ Ward et al.

BIOINFORMATICS (2004)

Review Pharmacology & Pharmacy

Utility of homology models in the drug discovery process

A Hillisch et al.

DRUG DISCOVERY TODAY (2004)

Article Medicine, General & Internal

Finding cures for tropical diseases: Is open source an answer?

SM Maurer et al.

PLOS MEDICINE (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemical Research Methods

ModLoop: automated modeling of loops in protein structures

A Fiser et al.

BIOINFORMATICS (2003)

Article Chemistry, Multidisciplinary

PRIMUS:: a Windows PC-based system for small-angle scattering data analysis

PV Konarev et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2003)

Article Biochemistry & Molecular Biology

Tools for comparative protein structure modeling and analysis

N Eswar et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Computer Science, Artificial Intelligence

Random forests

L Breiman

MACHINE LEARNING (2001)

Article Biochemical Research Methods

DBAli:: a database of protein structure alignments

MA Martí-Renom et al.

BIOINFORMATICS (2001)

Article Biochemistry & Molecular Biology

How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease

M Prabu-Jeyabalan et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)