bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rheology of cellulose/KSCN/ethylenediamine solutions and coagulation into filaments and films
Authors: Frey Margaret W. , Chan Hester , Carranco Kristen 
Published: June 2005

AbstractDissolution of cellulose in ethylenediamine/potassium thiocyanate (KSCN) was studied as a function of cellulose and KSCN concentration. Concentrations of up to 9% (w/w) cellulose were obtained. Large variations in solution rheology with salt and cellulose concentration were observed, and phases including flowing solutions and gels were identified visually. Rheological data indicated that viscosity decreased with increasing salt or cellulose concentration in certain composition ranges. Viscosity decrease with concentration increase is associated with either onset of liquid crystalline ordering or phase separation in the system. Both of these are quite likely in the cellulose/ethylenediamine/KSCN system, depending on composition. Additionally, comparison of loss (G′′) and storage (G′) moduli confirmed that compositions that exhibited gel behavior at zero shear became liquid at shear rates as low as 1 Hz. Solutions were coagulated into filaments and films using ethanol (CH3CH2OH) and methanol (CH3OH). Infrared spectroscopy (FTIR) indicated that significant quantities of KSCN salt remained in the fibers and films after coagulation. Subsequent washing removed residual KSCN and improved physical properties. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2013–2022, 2005
Nitrogen plasma modification on polyimide films for copper metallization on microelectronic flex substrates
Authors: Lin Yung‐Sen , Liu Huang‐Ming , Tsai Chung‐Wei 
Published: June 2005

AbstractSurface modification of polyimide films Kapton E(N) and Upilex S by nitrogen plasmas were investigated for their enhanced adhesion strength with sputtered coppers. Peel tests demonstrate this improvement, with peel strengths of 7 and 12 N/m for unmodified Kapton E(N) and Upilex S, and 1522 and 1401 N/m for nitrogen plasma‐modified Kapton E(N) and Upilex S at certain plasma conditions. Atomic force microscopy (AFM) and the sessile drop method indicated the surface roughness, and the surface energy of polyimide films were highly increased by nitrogen plasmas. This study shows the enhanced adhesion strengths of polyimide films with sputtered coppers by nitrogen plasmas, and these nitrogen plasmas were strongly affected by the surface characteristics of polyimide films. Electron spectroscopy for chemical analysis (ESCA) observed the increased surface energy on polyimide films by nitrogen plasmas was due to the increased surface composition of O and the increased chemical bond of CO. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2023–2038, 2005
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
Authors: Méndez Raúl , Leplae Raphaël , Lensink Marc F. , Wodak Shoshana J. 
Published: June 2005

AbstractThe current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional (3D) structure is reassessed by evaluating blind predictions, performed during 2003–2004 as part of Rounds 3–5 of the community‐wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Ten newly determined structures of protein–protein complexes were used as targets for these rounds. They comprised 2 enzyme–inhibitor complexes, 2 antigen–antibody complexes, 2 complexes involved in cellular signaling, 2 homo‐oligomers, and a complex between 2 components of the bacterial cellulosome. For most targets, the predictors were given the experimental structures of 1 unbound and 1 bound component, with the latter in a random orientation. For some, the structure of the free component was derived from that of a related protein, requiring the use of homology modeling. In some of the targets, significant differences in conformation were displayed between the bound and unbound components, representing a major challenge for the docking procedures. For 1 target, predictions could not go to completion. In total, 1866 predictions submitted by 30 groups were evaluated. Over one‐third of these groups applied completely novel docking algorithms and scoring functions, with several of them specifically addressing the challenge of dealing with side‐chain and backbone flexibility. The quality of the predicted interactions was evaluated by comparison to the experimental structures of the targets, made available for the evaluation, using the well‐agreed‐upon criteria used previously. Twenty‐four groups, which for the first time included an automatic Web server, produced predictions ranking from acceptable to highly accurate for all targets, including those where the structures of the bound and unbound forms differed substantially. These results and a brief survey of the methods used by participants of CAPRI Rounds 3–5 suggest that genuine progress in the performance of docking methods is being achieved, with CAPRI acting as the catalyst. Proteins 2005;60:150–169. © 2005 Wiley‐Liss, Inc.
The targets of CAPRI rounds 3–5
Authors: Janin Joël 
Published: June 2005

AbstractTen protein–protein complexes have been offered by X‐ray crystallographers as targets for structure prediction in Rounds 3–5 of the CAPRI experiment. They illustrate molecular recognition in several domains of biology: enzyme regulation, antigen–antibody recognition, signal transduction, and oligomer assembly. The targets presented various degrees of difficulty to the predictors, depending on their status (bound when components were taken from the complex, unbound when coming from independent structures of the free proteins), the amplitude of conformation changes, and the amount of biological information available. Predictors produced high‐quality models of 6 of the targets, good models of 3 others, and failed only in 1 case, where the conformation change was particularly large. This result demonstrates significant progress relative to earlier rounds of CAPRI. Proteins 2005;60:170–175. © 2005 Wiley‐Liss, Inc.
Classification of protein complexes based on docking difficulty
Authors: Vajda Sandor 
Published: June 2005

AbstractBased on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein–protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the targets of the CAPRI docking experiment. Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. The analysis indicates that CAPRI and other relatively large‐scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein–protein docking methods. Proteins 2005;60:176–180. © 2005 Wiley‐Liss, Inc.
CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock
Authors: Daily Michael D. , Masica David , Sivasubramanian Arvind , Somarouthu Sony , Gray Jeffrey J. 
Published: June 2005

AbstractCAPRI Rounds 3, 4, and 5 are the first public test of the published RosettaDock algorithm. The targets cover a wide range of sizes and shapes. For most targets, published biological information indicated the region of the binding site on at least one docking partner. The RosettaDock algorithm produced high accuracy predictions for three targets, medium‐accuracy predictions for two targets, and an acceptable prediction for one target. RosettaDock predicted all five targets with less than 450 residues to high or medium accuracy, but it predicted only one of seven targets with above 450 residues to acceptable accuracy. RosettaDock's high‐accuracy predictions for small to moderately large targets reveal the predictive power and fidelity of the algorithm, especially the high‐resolution refinement and scoring protocol. In addition, RosettaDock can predict complexes from at least one homology‐modeled docking partner with comparable accuracy to unbound cases of similar size. Larger targets present a more intensive sampling problem, and some large targets present repulsive barriers to entering the binding site. Ongoing improvements to RosettaDock's low‐resolution search may alleviate this problem. This first public test suggests that RosettaDock can be useful in a significant range of applications in biochemistry and cell biology. Proteins 2005;60:181–186. © 2005 Wiley‐Liss, Inc.
Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility
Authors: Schueler‐Furman Ora , Wang Chu , Baker David 
Published: June 2005

AbstractRosettaDock uses real‐space Monte Carlo minimization (MCM) on both rigid‐body and side‐chain degrees of freedom to identify the lowest free energy docked arrangement of 2 protein structures. An improved version of the method that uses gradient‐based minimization for off‐rotamer side‐chain optimization and includes information from unbound structures was used to create predictions for Rounds 4 and 5 of CAPRI. First, large numbers of independent MCM trajectories were carried out and the lowest free energy docked configurations identified. Second, new trajectories were started from these lowest energy structures to thoroughly sample the surrounding conformation space, and the lowest energy configurations were submitted as predictions. For all cases in which there were no significant backbone conformational changes, a small number of very low‐energy configurations were identified in the first, global search and subsequently found to be close to the center of the basin of attraction in the free energy landscape in the second, local search. Following the release of the experimental coordinates, it was found that the centers of these free energy minima were remarkably close to the native structures in not only the rigid‐body orientation but also the detailed conformations of the side‐chains. Out of 8 targets, the lowest energy models had interface root‐mean‐square deviations (RMSDs) less than 1.1 Å from the correct structures for 6 targets, and interface RMSDs less than 0.4 Å for 3 targets. The predictions were top submissions to CAPRI for Targets 11, 12, 14, 15, and 19. The close correspondence of the lowest free energy structures found in our searches to the experimental structures suggests that our free energy function is a reasonable representation of the physical chemistry, and that the real space search with full side‐chain flexibility to some extent solves the protein–protein docking problem in the absence of significant backbone conformational changes. On the other hand, the approach fails when there are significant backbone conformational changes as the steric complementarity of the 2 proteins cannot be modeled without incorporating backbone flexibility, and this is the major goal of our current work. Proteins 2005;60:187–194. © 2005 Wiley‐Liss, Inc.
Docking to single‐domain and multiple‐domain proteins: Old and new challenges
Authors: Ben‐Zeev E. , Kowalsman N. , Ben‐Shimon A. , Segal D. , Atarot T. , Noivirt O. , Shay T. , Eisenstein M. 
Published: June 2005

AbstractThe diverse selection of targets in the CAPRI experiments provides grounds for determining the limits of our rigid‐body docking program MolFit, and for extending it. We find that the sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled. Yet the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. This indicates that the selectivity of MolFit, which was optimized for docking of unbound X‐ray structures, and which relies on the availability of external data from biochemical and bioinformatic sources, needs readjustment in order to meet the challenges presented by NMR or modeled structures. A different challenge is presented by large global conformation changes such as movements of domains. We show that such changes can be accommodated within the rigid‐body approximation by employing rigid multibody multistage docking procedures. We also address the difficulty of ranking results from 2‐body and multibody docking scans in cases in which there are no external data favoring one option over the other. Proteins 2005;60:195–201. © 2005 Wiley‐Liss, Inc.
Modeling oligomers with Cn or Dn symmetry: Application to CAPRI target 10
Authors: Berchanski Alexander , Segal Dadi , Eisenstein Miriam 
Published: June 2005

AbstractThe abundance of oligomeric proteins makes them a frequent target for structure prediction. However, homologous proteins sometimes adopt different oligomerization states, rendering the prediction of structures of whole oligomers beyond the scope of comparative modeling. This obstacle can be overcome by combining comparative modeling of the single subunit of an oligomer with docking techniques, designed for predicting subunit–subunit interfaces. We present here algorithms for predicting the structures of homo‐oligomers with Cn or Dn (n > 2) symmetry. The prediction procedure includes a symmetry‐restricted docking step followed by a Cn or Dn oligomer‐forming step, in which the dimers from the docking step are assembled to oligomers. The procedure is applied to each of the crystallographically independent subunits in 8 Cn and 3 Dn oligomers, producing very accurate predictions. It is further applied to a single monomer of the tick‐borne encephalitis virus coat protein E (Target 10 of the CAPRI experiment). The predicted trimer ranked 30, obtained via rigid‐body geometric–hydrophobic docking followed by Cn oligomer formation, is very similar to the experimentally observed trimer formed by domain II of this protein. Furthermore, the predicted trimer formed from the separated domain I is also close to the experimental structure. Proteins 2005;60:202–206. © 2005 Wiley‐Liss, Inc.
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
Authors: Wiehe Kevin , Pierce Brian , Mintseris Julian , Tong Wei Wei , Anderson Robert , Chen Rong , Weng Zhiping 
Published: June 2005

AbstractWe present an evaluation of the results of our ZDOCK and RDOCK algorithms in Rounds 3, 4, and 5 of the protein docking challenge CAPRI. ZDOCK is a Fast Fourier Transform (FFT)‐based, initial‐stage rigid‐body docking algorithm, and RDOCK is an energy minimization algorithm for refining and reranking ZDOCK results. Of the 9 targets for which we submitted predictions, we attained at least acceptable accuracy for 7, at least medium accuracy for 6, and high accuracy for 3. These results are evidence that ZDOCK in combination with RDOCK is capable of making accurate predictions on a diverse set of protein complexes. Proteins 2005;60:207–213. © 2005 Wiley‐Liss, Inc.
Protein–protein docking benchmark 2.0: An update
Authors: Mintseris Julian , Wiehe Kevin , Pierce Brian , Anderson Robert , Chen Rong , Janin Joël , Weng Zhiping 
Published: June 2005

AbstractWe present a new version of the Protein–Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound–unbound cases, with 52 rigid‐body cases, 13 medium‐difficulty cases, and 7 high‐difficulty cases with substantial conformational change. In addition, we retained 12 antibody–antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2. Proteins 2005;60:214–216. © 2005 Wiley‐Liss, Inc.
Approaching the CAPRI challenge with an efficient geometry‐based docking
Authors: Inbar Yuval , Schneidman‐Duhovny Dina , Halperin Inbal , Oron Assaf , Nussinov Ruth , Wolfson Haim J. 
Published: June 2005

AbstractThe last 3 rounds (3–5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large‐scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry‐based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side‐chain position refinement and the introduction of flexibility for both docking partners. Proteins 2005;60:217–223. © 2005 Wiley‐Liss, Inc.
Geometry‐based flexible and symmetric protein docking
Authors: Schneidman‐Duhovny Dina , Inbar Yuval , Nussinov Ruth , Wolfson Haim J. 
Published: June 2005

AbstractWe present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.
Performance of the first protein docking server ClusPro in CAPRI rounds 3–5
Authors: Comeau Stephen R. , Vajda Sandor , Camacho Carlos J. 
Published: June 2005

AbstractTo evaluate the current status of the protein–protein docking field, the CAPRI experiment came to life. Researchers are given the receptor and ligand 3‐dimensional (3D) coordinates before the cocrystallized complex is published. Human predictions of the complex structure are supposed to be submitted within 3 weeks, whereas the server ClusPro has only 24 h and does not make use of any biochemical information. From the 10 targets analyzed in the second evaluation meeting of CAPRI, ClusPro was able to predict meaningful models for 5 targets using only empirical free energy estimates. For two of the targets, the server predictions were assessed to be among the best in the field. Namely, for Targets 8 and 12, ClusPro predicted the model with the most accurate binding‐site interface and the model with the highest percentage of nativelike contacts, among 180 and 230 submissions, respectively. After CAPRI, the server has been further developed to predict oligomeric assemblies, and new tools now allow the user to restrict the search for the complex to specific regions on the protein surface, significantly enhancing the predictive capabilities of the server. The performance of ClusPro in CAPRI Rounds 3–5 suggests that clustering the low free energy (i.e., desolvation and electrostatic energy) conformations of a homogeneous conformational sampling of the binding interface is a fast and reliable procedure to detect protein–protein interactions and eliminate false positives. Not including targets that had a significant structural rearrangement upon binding, the success rate of ClusPro was found to be around 71%. Proteins 2005;60:239–244. © 2005 Wiley‐Liss, Inc.
Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets
Authors: Camacho Carlos J. 
Published: June 2005

AbstractThe CAPRI‐II experiment added an extra level of complexity to the problem of predicting protein–protein interactions by including 5 targets for which participants had to build or complete the 3‐dimensional (3D) structure of either the receptor or ligand based on the structure of a close homolog. In this article, we describe how modeling key side‐chains using molecular dynamics (MD) in explicit solvent improved the recognition of the binding region of a free energy– based computational docking method. In particular, we show that MD is able to predict with relatively high accuracy the rotamer conformation of the anchor side‐chains important for molecular recognition as suggested by Rajamani et al. (Proc Natl Acad Sci USA 2004;101:11287–11292). As expected, the conformations are some of the most common rotamers for the given residue, while latch side‐chains that undergo induced fit upon binding are forced into less common conformations. Using these models as starting conformations in conjunction with the rigid‐body docking server ClusPro and the flexible docking algorithm SmoothDock, we produced valuable predictions for 6 of the 9 targets in CAPRI‐II, missing only the 3 targets that underwent significant structural rearrangements upon binding. We also show that our free energy– based scoring function, consisting of the sum of van der Waals, Coulombic electrostatic with a distance‐dependent dielectric, and desolvation free energy successfully discriminates the nativelike conformation of our submitted predictions. The latter emphasizes the critical role that thermodynamics plays on our methodology, and validates the generality of the algorithm to predict protein interactions. Proteins 2005;60:245–251. © 2005 Wiley‐Liss, Inc.
ATTRACT: Protein–protein docking in CAPRI using a reduced protein model
Authors: Zacharias Martin 
Published: June 2005

AbstractProtein–protein complex structures have been predicted for CAPRI Rounds 3 and 5 using a reduced protein model. Proteins are represented by up to 3 pseudoatoms per amino acid. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to another protein. The reduced protein model allows one to perform systematic docking minimization of many thousand start structures in reasonable computer time. Flexibility of critical surface side‐chains can be accounted for by a multiple conformational copy approach. The multicopy approach allows simultaneous adjustment of side‐chain conformations and optimization of translational and rotational degrees of freedom of one protein with respect to the partner during docking. For 3 (Targets 8, 14, and 19) out of 5 CAPRI targets, the approach resulted in predictions in close agreement with experiment [root‐mean‐square deviation (RMSD) of backbone atoms within 10 Å of the protein–protein interface < 1.8 Å]. The comparison of predicted and experimental structures of the CAPRI targets indicates that besides local conformational changes (e.g., changes in side‐chain conformations), global conformational changes of the protein backbone can be critical for complex formation. These conformational changes not accounted for during docking are a likely reason for the unrealistic predictions in 2 cases (Targets 9 and 18). Proteins 2005;60:252–256. © 2005 Wiley‐Liss, Inc.