Integrative structure modeling with the Integrative Modeling Platform.
Benjamin Webb,Shruthi Viswanath,Massimiliano Bonomi,Riccardo Pellarin,Charles H. Greenberg,Daniel J. Saltzberg,Andrej Sali +6 more
TLDR
The Integrative Modeling Platform (IMP) as mentioned in this paper is an open source software suite for integrative structure modeling, which casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models.Abstract:
Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (IMP) (https://integrativemodeling.org), and demonstrate its use. This article is protected by copyright. All rights reserved.read more
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Journal ArticleDOI
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Julia Koehler Leman,Brian D. Weitzner,Brian D. Weitzner,Steven M. Lewis,Steven M. Lewis,Jared Adolf-Bryfogle,Nawsad Alam,Rebecca F. Alford,Melanie L. Aprahamian,David Baker,Kyle A. Barlow,Patrick Barth,Patrick Barth,Benjamin Basanta,Brian J. Bender,Kristin Blacklock,Jaume Bonet,Jaume Bonet,Scott E. Boyken,Phil Bradley,Christopher Bystroff,Patrick Conway,Seth Cooper,Bruno E. Correia,Bruno E. Correia,Brian Coventry,Rhiju Das,René M. de Jong,Frank DiMaio,Lorna Dsilva,Roland L. Dunbrack,Alex Ford,Brandon Frenz,Darwin Y. Fu,Caleb Geniesse,Lukasz Goldschmidt,Ragul Gowthaman,Jeffrey J. Gray,Dominik Gront,Sharon L. Guffy,Scott Horowitz,Po-Ssu Huang,Thomas Huber,Timothy M. Jacobs,Jeliazko R. Jeliazkov,David K. Johnson,Kalli Kappel,John Karanicolas,Hamed Khakzad,Hamed Khakzad,Karen R. Khar,Sagar D. Khare,Firas Khatib,Alisa Khramushin,Indigo Chris King,Robert Kleffner,Brian Koepnick,Tanja Kortemme,Georg Kuenze,Brian Kuhlman,Daisuke Kuroda,Jason W. Labonte,Jason W. Labonte,Jason K. Lai,Gideon Lapidoth,Andrew Leaver-Fay,Steffen Lindert,Thomas W. Linsky,Nir London,Joseph H. Lubin,Sergey Lyskov,Jack Maguire,Lars Malmström,Lars Malmström,Lars Malmström,Enrique Marcos,Orly Marcu,Nicholas A. Marze,Jens Meiler,Rocco Moretti,Vikram Khipple Mulligan,Santrupti Nerli,Christoffer Norn,Shane O’Conchúir,Noah Ollikainen,Sergey Ovchinnikov,Michael S. Pacella,Xingjie Pan,Hahnbeom Park,Ryan E. Pavlovicz,Manasi A. Pethe,Brian G. Pierce,Kala Bharath Pilla,Barak Raveh,P. Douglas Renfrew,Shourya S. Roy Burman,Aliza B. Rubenstein,Marion F. Sauer,Andreas Scheck,Andreas Scheck,William R. Schief,Ora Schueler-Furman,Yuval Sedan,Alexander M. Sevy,Nikolaos G. Sgourakis,Lei Shi,Justin B. Siegel,Daniel-Adriano Silva,Shannon Smith,Yifan Song,Amelie Stein,Maria Szegedy,Frank D. Teets,Summer B. Thyme,Ray Yu-Ruei Wang,Andrew M. Watkins,Lior Zimmerman,Richard Bonneau +117 more
TL;DR: This Perspective reviews tools developed over the past five years in the Rosetta software, including over 80 methods, and discusses improvements to the score function, user interfaces and usability.
Inferential Structure Determination
Wolfgang Rieping,Michael Habeck +1 more
TL;DR: In this paper, the authors used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision, and implemented this approach by using Markov chain Monte Carlo techniques.
Journal ArticleDOI
Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates.
TL;DR: At atomistic and coarse-grained simulation studies of amyloid peptides in their monomeric, oligomersic, and fibrillar states are reviewed and particular emphasis is given to the challenges one faces to characterize at atomic level of detail the conformational space of disordered (poly)peptides and their aggregation.
Journal ArticleDOI
In-cell architecture of the nuclear pore and snapshots of its turnover.
Matteo Allegretti,Christian E. Zimmerli,Vasileios Rantos,Florian Wilfling,Paolo Ronchi,Herman K.H. Fung,Chia-Wei Lee,Wim J. H. Hagen,Beata Turoňová,Kai Karius,Mandy Börmel,Xiaojie Zhang,Christoph W. Müller,Yannick Schwab,Julia Mahamid,Boris Pfander,Jan Kosinski,Martin Beck +17 more
TL;DR: In-cell structural studies in Saccharomyces cerevisiae reveal that the configuration of the Nup159 complex is a key determinant of the mRNA export function of the nuclear pore complex, and suggest a model of NPC turnover in which NPC-containing vesicles bud off from the nuclear envelope before degradation by the autophagy machinery.
Journal ArticleDOI
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
Eitan Lerner,Anders Barth,Jelle Hendrix,Benjamin Ambrose,Victoria Birkedal,Scott C. Blanchard,Richard Börner,Hoi Sung Chung,Thorben Cordes,Timothy D. Craggs,Ashok A. Deniz,Jiajie Diao,Jingyi Fei,Ruben L. Gonzalez,Irina V. Gopich,Taekjip Ha,Christian A. Hanke,Gilad Haran,Nikos S. Hatzakis,Sungchul Hohng,Seok Cheol Hong,Thorsten Hugel,Antonino Ingargiola,Chirlmin Joo,Achillefs N. Kapanidis,Harold D. Kim,Ted A. Laurence,Nam Ki Lee,Tae Hee Lee,Edward A. Lemke,Emmanuel Margeat,Jens Michaelis,Xavier Michalet,Sua Myong,Daniel Nettels,Thomas-Otavio Peulen,Evelyn Ploetz,Yair Razvag,Nicole C. Robb,Benjamin Schuler,Hamid Soleimaninejad,Chun Tang,Reza Vafabakhsh,Don C. Lamb,Claus A. M. Seidel,Shimon Weiss +45 more
TL;DR: The state-of-the-art in single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics as mentioned in this paper, which has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation.
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