A5028845140- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Nuclear Structure and Function
- RNA modifications and cancer
- Microbial Metabolic Engineering and Bioproduction
- Glycosylation and Glycoproteins Research
- Bioinformatics and Genomic Networks
- Advanced Electron Microscopy Techniques and Applications
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Monoclonal and Polyclonal Antibodies Research
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Ubiquitin and proteasome pathways
- Fungal and yeast genetics research
- vaccines and immunoinformatics approaches
- Drug Transport and Resistance Mechanisms
- Genomics and Chromatin Dynamics
- SARS-CoV-2 and COVID-19 Research
- Microtubule and mitosis dynamics
- Peptidase Inhibition and Analysis
- Amino Acid Enzymes and Metabolism
- Biochemical and Molecular Research
University of California, San Francisco
2016-2025
University of California System
2014-2025
QB3
2016-2025
Quantitative BioSciences
2013-2025
Deutsches Elektronen-Synchrotron DESY
2024
Max Planck Institute of Biochemistry
2023
Hebrew University of Jerusalem
2021
Universidad Católica de Santa Fe
2020
Worldwide Protein Data Bank
2019
Rockefeller University
1996-2018
Abstract Functional characterization of a protein sequence is one the most frequent problems in biology. This task usually facilitated by accurate three‐dimensional (3‐D) structure studied protein. In absence an experimentally determined structure, comparative or homology modeling can sometimes provide useful 3‐D model for that related to at least known structure. Comparative predicts given (target) based primarily on its alignment more proteins (templates). The prediction process consists...
Abstract Comparative protein structure modeling predicts the three‐dimensional of a given sequence (target) based primarily on its alignment to one or more proteins known (templates). The prediction process consists fold assignment, target‐template alignment, model building, and evaluation. This unit describes how calculate comparative models using program MODELLER use ModBase database such models, discusses all four steps modeling, frequently observed errors, some applications. Modeling...
Abstract Functional characterization of a protein sequence is common goal in biology, and usually facilitated by having an accurate three‐dimensional (3‐D) structure the studied protein. In absence experimentally determined structure, comparative or homology modeling can sometimes provide useful 3‐D model for that related to at least one known structure. Comparative predicts given (target) based primarily on its alignment more proteins (templates). The prediction process consists fold...
Protein structures in the Data Bank provide a wealth of data about interactions that determine native states proteins. Using probability theory, we derive an atomic distance-dependent statistical potential from sample does not depend on any adjustable parameters (Discrete Optimized Energy, or DOPE). DOPE is based improved reference state corresponds to noninteracting atoms homogeneous sphere with radius dependent structure; it thus accounts for finite and spherical shape structures. The was...
Abstract Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves accuracy of predictions structures. The positions all nonhydrogen atoms are optimized fixed environment with respect to pseudo energy function. sum many spatial restraints include bond length, angle, improper dihedral angle terms from CHARMM‐22 force field, statistical preferences for main‐chain...
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role these proteins will require knowledge their structure and function. Although experimental determination methods providing high-resolution information about a subset proteins, computational prediction provide valuable for large fraction sequences whose structures not be determined experimentally. The first class protein methods, including threading comparative modeling, rely on...
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center global PDB archive and a founding member of Worldwide partnership, serves tens thousands depositors in Americas Oceania makes 3D macromolecular structure available at no charge without restrictions to millions RCSB.org users around world, including >660 000 educators, students members curious public using PDB101.RCSB.org. include structural biologists crystallography,...
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and assessment (http://salilab.org/modeller/). currently contains 10,355,444 reliable domains in 2,421,920 unique sequences. allows users to update demand, request additional sequences through interface the ModWeb server...
Abstract We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and eosinophil neurotoxin that were calculated by M ODELLER , a program for comparative modeling satisfaction spatial restraints. The have good stereochemistry are at least as similar to the crystallographic structures closest template structures. largest errors occur in regions not aligned correctly or where correct structure. These correspond predominantly exposed loops,...
Functional characterization of a protein sequence is one the most frequent problems in biology. This task usually facilitated by accurate three-dimensional (3-D) structure studied protein. In absence an experimentally determined structure, comparative or homology modeling can sometimes provide useful 3-D model for that related to at least known structure. Comparative predicts given (target) based primarily on its alignment more proteins (templates). The prediction process consists fold...
ModLoop is a web server for automated modeling of loops in protein structures. The input the atomic coordinates structure Protein Data Bank format, and specification starting ending residues one or more segments to be modeled, containing no than 20 total. output non-hydrogen atoms modeled segments. A user provides via simple interface, receives by e-mail. relies on loop routine MODELLER that predicts conformations satisfaction spatial restraints, without relying database known For rapid...
Abstract Comparative protein structure modeling predicts the three‐dimensional of a given sequence (target) based primarily on its alignment to one or more proteins known (templates). The prediction process consists fold assignment, target‐template alignment, model building, and evaluation. This unit describes how calculate comparative models using program MODELLER use ModBase database such models, discusses all four steps modeling, frequently observed errors, some applications. Modeling...
A major challenge in structural biology is to characterize structures of proteins and their assemblies solution. At low resolution, such a characterization may be achieved by small angle x-ray scattering (SAXS). Because SAXS analyses often require comparing profiles calculated from many atomic models against those determined experiment, rapid accurate profile computation molecular needed. We developed fast open-source (FoXS) for computation. To match the experimental within noise, FoXS...